This paper studies the influencing factors and transmission mechanism of science education in rural primary schools based on the data gathered from rural teachers in 13 districts of Heilongjiang province. The study shows that the situation of science education in rural primary schools is satisfactory, and there are no obvious differences in the type and the location of schools. Primary science education could be significantly influenced by rural school teaching capital; rural school teaching capital indirectly improves the implementation effect of primary school science education through the intermediary role of social participation, meanwhile, the quality monitoring of curriculum implementation has an enhanced regulatory role in the positive impact of rural school teaching capital on social participation. Given the limited teaching capital, a number of measures shall be taken to create a sound atmosphere of science education from the perspective of value perception in rural schools, to enhance the teaching capital of science education through outside help, and to improve the monitoring system of teaching quality for promoting an effective implementation of science education in primary schools.