Based on a literature review of property rights and ecological property rights and the analysis of deep reasons for low efficiency of the operation of ecological property rights system in China, it proposes theoretical basis of optimal institutional arrangement of ecological property rights taking non-development ownership as the core concept and possible practice routes, and employs multi-stage bilateral auction model with embedded incentive mechanisms based on game theory to confirm the existence of Bayesian equilibrium price of non-development ownership. It arrives at the following conclusions:firstly, the conflicts of basic interests in ecological field result from extremely strong positive externalities, and non-internalization or non-marketization of ecological products, and are the root causes of the failure of property rights system; secondly, according to the separability of property rights, the property rights system covering non-exploitable ownership and exploitable ownership can be constructed; thirdly, the construction of market taking non-development ownership as trading products can be regarded as the optimal route of the property rights system and simultaneously is the effective route of the internalization of positive externalities of ecological products; fourthly, government ecological purchase is the effective realization form of the optimal route of the property rights system. When introducing incentive mechanisms, multi-stage bilateral auction model based on incomplete information can achieve theoretical purchase price of Bayesian equilibrium. The above conclusions can be taken as policy instruments of the reform of the property rights system.