In the post-crisis era, the uncertainties faced by the changing world economy are increasing. How does the rising uncertainty affect economic development? Existing studies have made substantial progress in the measurement, causes and effects of uncertainty, but no consensus has yet been reached. Based on the real option effect, the rising uncertainty increases the cost of the real asset investment and reduces the investment expenditure. Based on the growth option effect, the rising uncertainty increases the financial asset investment. This paper uses the natural test provided by China’s supply-side structural reform policy to analyze the mechanism of uncertainty impacts on the micro-enterprise investment behavior. Based on the 2013-2016 quarterly data of China’s A-share listed companies, we construct a double difference model for empirical testing. The increase in uncertainty significantly reduces the investment in fixed assets, technology assets and physical assets of enterprises, but increases the investment in corporate financial assets. This phenomenon is more obvious in the intervention group. The results of the double-difference model test support that uncertainty has a significant negative impact on the fixed asset investment and inventory investment of the intervention group. Among state-owned enterprises, uncertainty has a significant impact on the technology asset investment and inventory investment of the intervention group. Among private enterprises, uncertainty has a significant impact on the fixed asset investment of the intervention group. After the supply-side structural reform policy, corporate external borrowing financing is constrained, further inhibiting corporate physical asset investment activities. On the contrary, enterprises have increased the scale of the financial asset investment after the supply-side structural reform policy. This possible intermediary path is that the external financing ability of enterprises is constrained and affects the allocation orientation on different assets. In general, the supply-side structural reform policy contributes to the company’s value. However, the current investment activities of fixed assets, technology assets, inventory physical assets do not contribute to the company’s value. The financial asset investment is conducive to the company’s value growth, confirming the micro-subjects to follow the capital profit-seeking motives. The test is re-examined with a variety of robustness tests. The results are consistent with the previous ones, indicating that the research conclusions in this paper are robust and reliable. This paper examines the uncertainty impacts on the different capital forms of micro-enterprise investment by using policy events, and provides more direct empirical evidence for the study of uncertainty causality and a meaningful reference for the economic impact of the current global uncertain events.