Abstract: The binary household registration system plays a key role in the development of endowment insurance system in China. Comparing the differences of rural and urban endowment insurance coverage ratio and payment per capital level before and after the household registration reform, we find that breaking the household registration limit will facilitate the construction of endowment insurance integration, decrease its inequality under the urban and rural system, and create the advantageous conditions for the floating population. Meanwhile, by comparative analysis of the positive role and negative influence that the household registration system plays on the endowment insurance system in China, it is suggested that our government should establish urban-rural integrated organizations, create " Internet +” data platform, and carry out " all-in-one-card” of endowment insurance so as to eliminate the negative influences of household registration system reform on endowment insurance system and ensure the healthy development of the endowment insurance system.