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Straw incorporation has been widely recommended as an effective management practice to increase soil nitrogen stocks in agroecosystems worldwide. However, the overall trend and magnitude of changes in various soil organic nitrogen fractions in response to crop residue return and their contribution to soil nitrogen sequestration remain uncertain. Here, we show through a long-term experiment (12 years) that straw return increased soil total nitrogen and soil nitrogen sequestration rate by 20.01% and 120.95%, respectively. Ammonia nitrogen, amino acid nitrogen, and amino sugar nitrogen were affected by straw and its interaction with year, and increased by 43.08%, 27.70%, and 46.56%, respectively, with the highest growth rate in amino acid nitrogen (10.51 mg kg−1 yr−1). Furthermore, redundancy analyses showed that soil total organic carbon and C:N ratio were the major factors explaining the variations in soil organic nitrogen fractions, which increased by 46.22% and 21.75%, respectively. The structural equation model further revealed that amino acid nitrogen was a pivotal driver of soil nitrogen sequestration, because the soil C:N ratio indirectly influenced soil nitrogen sequestration via affecting the accumulation of amino acid nitrogen. Our results suggest that long-term straw return can improve nitrogen sequestration by accelerating the accumulation of amino acid nitrogen and that soil nitrogen storage and supply capacity may be improved by adopting straw incorporation and other appropriate management practices to regulate soil stoichiometry. • Straw return promoted soil nitrogen sequestration. • Straw return increased soil organic nitrogen fractions. • Straw return increased the soil TOC and C:N ratio. • TOC and C:N ratio explained the variations of soil organic nitrogen fractions. • Amino acid nitrogen was a pivotal driver of soil nitrogen sequestration. [ABSTRACT FROM AUTHOR]