Summary: The mineralization of crop residue-nitrogen (N) is important for sustainable N supply to subsequent crops. However, the microbial mechanisms regarding residue-N mineralization over growth seasons are still unclear. We amended 15N-labelled maize and soybean residues to a Mollisol soil and found that, after three growth seasons, soybean plants utilized 43% and 37% of soybean and maize residue-N, respectively. Approximately 10.5% of soybean and 18.6% of maize residue-N were recovered in the labile N pools in soil. Over time, 82% of soybean residue-N was mineralized compared with 66% for maize residue-N. Greater increases in abundances of microbial functional genes involved in organic C decomposition, N mineralization, N2 fixation, and denitrification were observed in the soybean residue compared to the maize residue treatment. The study implies that soybean residue amendment may lower fertilizer N input more effectively than maize residue, considering the N balance between crop demand and soil supply in farming Mollisols.