Abstract: Despite increasing application of Chinese milk vetch (MV) and rice straw (RS), their combined effects on soil aggregate structure and nutrient storage are poorly understood. A field experiment was conducted to evaluate the effects of co-incorporation of MV and RS on rice yield and soil fertility. Five different fertilization regimes were adopted over a 3-year period. Chemical nitrogen (N) fertilizer was applied at a conventional rate (100%N) and a 40% reduced rate alone (60%N) or combined with MV (60%NMV), RS (60%NRS), and MV plus RS (60%NMVRS). Compared with the 100%N treatment, there were no distinct yield losses in the 60%NMV and 60%NMVRS treatments. Incorporation of organic amendments altered the composition of soil aggregates, as indicated by the increase of large (> 2 mm) and small (0.25–2 mm) macroaggregates and decrease of silt and clay (< 0.053 mm). The organic carbon and nitrogen storage were respectively decreased by 9.2% and 13.9% in the 60%N treatment, and this effect was diminished in the 60%NMVRS treatment, rather than the 60%NMV or 60%NRS treatment. The carbon and nitrogen storage in soil macroaggregates increased in response to organic amendments, and their peak values were observed in the 60%NMVRS treatment. Random forest analysis identified carbon and nitrogen storage in soil macroaggregates as the major contributors to rice yield. Continuous co-incorporation of Chinese milk vetch and rice straw maintained rice productivity with reduced nitrogen application as a consequence of improved soil aggregation (> 0.25 mm), increased carbon and nitrogen storage in macroaggregates, and enhanced nutrient availability.Graphical Abstract: