Research Purpose: This study aimed to explore the effect of China’s New Rural Pension (NRP) on the physical and mental health of rural children from the perspective of intergenerational care, and to examine whether family childcare types and the child’s gender affect the relationships between social pensions and the physical and mental health of rural children. Methods: We used data from the 2016 China Family Panel Studies (CFPS) of the China Social Science Survey Center, a nationally representative sample at the individual, family, and county levels from 25 provinces (cities and districts) in China. A total of 2142 sets of valid samples of children, the elderly, family economic and social conditions, and basic family information were retained after data screening. The regression discontinuity (RD) method was employed for the statistical analyses. Results: The NRP had a significant effect on both the mental health (β = −2.818, p < 0.1) and physical health (β = −2.214, p < 0.1) of rural children. This effect varied with the family childcare type and child’s gender. Conclusions: We reveal a positive effect of the NRP on the physical and mental health of rural children. Therefore, the establishment of a social pension system may be used as an effective approach to enhance the health of rural children. The impact of the NRP on the physical and mental health of children differs with the family childcare type and their gender, which should be taken into consideration when using social pensions to enhance child health.