Abstract: The fund operation of policy guidance funds is the innovation of urban investment and financing. Under the new normal state of slow fiscal revenue growth, rigid expenditure growth and widening gap between income and expenditure, it is of practical significance in raising funds for infrastructure construction, controlling government debt, activating social capital and promoting the reform of state-owned enterprises’ mixed ownership. Taking Nanjing municipal fund operation of infrastructure guidance fund as an example and based on the theory of transaction cost economics, the article analyzes the negative impact of the transaction costs in the fund operation, imperfect contract and asset specificity, and reveals the reason why social capital is stuck in holdup problem after a fundamental change. On this basis, five comprehensive strategies are proposed: reasonably guiding social capital into public goods and services that are relatively low in asset specificity; increasing the transparency of the fund operation; improving the supervisory ability of the fund in accordance with the law; establishing the operation mode of the master-feeder funds and the last is to consolidate the policy guidance fund.