Innovation is not only an important channel for enterprises to obtain excess returns (Porter, 1992), but also a key driver of sustainable economic growth in the country (Solow, 1957). Especially in the context of the current rising costs, weak export growth and trade disputes, it is crucial to the continued growth of the economy and the stable development of society. Unlike capital investment, innovation is accompanied by longer development cycles and higher uncertainty. Therefore, innovation investment and its efficiency are influenced by both the factor resources owned by enterprises and the incentives of executives. On the one hand, enterprise innovation is generally faced with financing constraints and operational risks, while diversification is conducive to the formation of the internal capital market and the knowledge spillover effect (Huang and Chen, 2011), which in turn promotes enterprises’ long-term and sustained innovation investment. On the other hand, management will also use scarce resources for expanding scale or gaining short-term profits on the basis of personal interests, thus reducing R&D investment of enterprises (Wang, et al., 2017). In addition, the " strategic” R&D investment in non-main business during the diversification (Li and Zheng, 2016) may further squeeze out innovation investment in main business.　　Based on the detailed data of R&D investment of Chinese listed companies from 2007 to 2015, using multiple regression methods, the empirical evidence shows that: (1) Diversification is negatively correlated with R&D, and the correlation exists only in main business, especially in state-owned enterprises (SOEs). Further, non-main business R&D is also negatively related to main business R&D, and such correlation exists only in private enterprises. (2) Strong government intervention and large promotion pressure of SOE executives strengthen the crowding-out effect of SOE diversification on main business R&D; the ownership discrimination of private enterprises’ resource strengthens the extrusion effect of non-main business R&D on main business. (3) Main business R&D investment is conducive to increasing invention patents, which is reflected in the increase of innovation efficiency. Diversification reduces innovation efficiency (which only exists in SOEs, especially in SOEs with stronger government intervention and higher promotion pressure). Non-main business R&D reduces invention patents, which is reflected in the loss of innovation efficiency (which only exists in private enterprises, especially those not supported by industrial policies).　　The possible contributions of this paper are as follows: (1) It not only summarizes and discusses the possible impact of diversification directly on enterprise innovation, but also further divides R&D investment into main business and non-main business, summarizing the promotion and extrusion effect of non-main business R&D on main business R&D, which explains the paradox of relevant research and enriches the existing literature. (2) In the context of China’s special system, based on the perspective of ownership differences, it reveals the " dual” innovation efficiency loss of diversification in the property rights level. (3) Based on the innovation, it reveals the specific role of diversification, and also provides a partial explanation for the existing disputes over the discount and premium of diversification.　　The possible policy implications are as follows: (1) There are a different way of enterprise transformation between R&D investment in main business and diversification. Combining their own resource endowments and market environment, different enterprises need to weigh and select the successful path of transformation. (2) Innovation cannot conduct without resources, so it is imperative to improve the business environment and create a favorable environment for innovation. On the one hand, we should promote the separation of the government and enterprises, reduce the government intervention on enterprises, adjust and optimize the performance system of SOEs’ executives, and continuously strengthen the internal governance and external supervision for SOEs to facilitate the innovation; on the other hand, it is vital to match innovation intentions and capabilities through the market-oriented allocation of resources, and accelerate private enterprise innovation. (3) Enterprises also need to focus on the optimal allocation of innovative assets, so that they can flow to the projects related to main business, which can improve the innovation efficiency and optimize the allocation of resources as well as promote the continuous growth of the macro economy.