The diffusion of new energy vehicles (NEVs), such as battery electric vehicles (BEVs) and fuel cell vehicles (FCVs), is critical to the transportation sector’s deep decarbonization. The cost of energy chains is an important factor in the diffusion of NEVs. Although researchers have addressed the technological learning effect of NEVs and the life cycle emissions associated with the diffusion of NEVs, little work has been conducted to analyze the life cycle costs of different energy chains associated with different NEVs in consideration of technological learning potential. Thus, relevant information on investment remains insufficient to promote the deployment of NEVs. This study proposes a systematic framework that includes various (competing or coordinated) energy chains of NEVs formed with different technologies of power generation and transmission, hydrogen production and transportation, power-to-liquid fuel, and fuel transportation. The levelized costs of three typical carbon-neutral energy chains are investigated using the life cycle cost model and considering the technological learning effect. Results show that the current well-to-pump levelized costs of the energy chains in China for BEVs, FCVs, and internal combustion engine vehicles (ICEVs) are approximately 3.60, 4.31, and 2.21 yuan/GJ, respectively, and the well-to-wheel levelized costs are 4.50, 6.15, and 7.51 yuan/GJ, respectively. These costs primarily include raw material costs, and they vary greatly for BEVs and FCVs from resource and consumer costs. In consideration of the technological learning effect, the energy chains’ well-to-wheel levelized costs are expected to decrease by 24.82% for BEVs, 27.12% for FCVs, and 19.25% for ICEVs by 2060. This work also summarizes policy recommendations on developing energy chains to promote the diffusion of NEVs in China.