Clean energy vehicles (CEVs), e.g., battery electric vehicles (BEVs) and fuel cell electric vehicles (FCEVs), are being adopted gradually to substitute for internal combustion engine vehicles (ICEVs) around the world. The fueling infrastructure is one of the key drivers for the development of the CEV market. When the government develops funding policies to support the fueling infrastructure development for FCEVs and BEVs, it has to assess the effectiveness of different policy options and identify the optimal policy combination, which is very challenging in transportation research. In this paper, we develop a system dynamics model to study the feedback mechanism between the fueling infrastructure funding policies and the medium- to long-term diffusion of FCEVs and BEVs, and the competition between FCEVs and BEVs based on relevant policy and market data in Guangzhou, China. The results of the modeling analysis are as follows. (1) Funding hydrogen refueling stations and public charging piles has positive implications for achieving the substitution of CEVs for ICEVs. (2) Adjusting the funding ratio of hydrogen refueling stations and public charging piles or increasing the funding budget and extending the funding cycle does not have a significant impact on the overall substitution of CEVs for ICEVs but only impacts the relative competitive advantage between FCEVs and BEVs. (3) An equal share of funding for hydrogen refueling stations and public charging piles would have better strategic value for future net-zero-emissions urban transportation. (4) Making a moderate-level full investment in hydrogen refueling stations, coupled with hydrogen refueling subsidies, can provide the ideal conditions for FCEV diffusion.