The knowledge of the contribution of carbon (C) released by growing roots to soil is essential to better understand the terrestrial C cycling and optimally manage soil organic matter in ecosystems. However, little information has been gained on quantifying the distribution of photosynthetically fixed C in the plant–soil system and its contribution to soil C over a growing season in soybean-grown Mollisols, the main soil type in Northeast China. In a pulse-chase labelling experiment, soybean plants grown in Mollisols were labelled with 13CO2 at various growth stages. More than 3/4 of fixed 13C was observed in shoots at Day 0 after labelling, and then the fixed 13C was continually exported from shoots, showing that 7.5% of 13C fixed at V4 (fourth node) and 71.1% at R6 (full seed stage) remained in shoots by the end of the growing season. The 13C recovery in roots decreased over the same period, while soil 13C was significantly increased. The allocation of 13C fixed at different growth stages to underground (roots and soil) varied at the end of the growing season, showing that 13C retained in roots and soil was 6.0 and 12.4% of the net assimilation at V4, compared with 1.4 and 2.1% of that at R6, respectively. Nodules, however, had the highest demand for C at R4 (full pod stage). The contribution of shoot C assimilation to the soil C pool was similar at the growth stages up to R5 before a sharp decrease at R6, and the cumulative contribution reached 93% at R5. Over the whole growing season, it was estimated that ~210 kg of photosynthetically fixed C per ha was accumulated in soil. This indicates that the C flow from soybean plants to soil during growth is a non-negligible source of C pool in Mollisols, and the majority of the C efflux occurs during V4–R5.