To investigate effects of biomass materials on soil water-stable aggregates and screen optimal methods to improve the structure of heavy clay soil, research was conducted using heavy clay soil at the bottom of rivers and lakes as the research object. Eight treatments were set up: non-applied materials (CK), maize straw (MS), Trichoderma harzianum (TH), enzymatic hydrolysis fish protein (FP), Trichoderma harzianum + enzymatic hydrolysis fish protein (TH+FP), maize straw + Trichoderma harzianum (MS+TH), maize straw + enzymatic hydrolysis fish protein (MS+FP) and maize straw + Trichoderma harzianum + enzymatic hydrolysis fish protein (MS+TH+FP). An indoor culture experiment was carried out to explore effects of different biomass material combinations on the composition of soil water-stable aggregates and their potential mechanisms. Compared to CK, macroaggregate content and aggregate stability significantly increased at both 90 d and 180 d for all treatments. Macroaggregate content of MS decreased at 180 d compared to 90 d, and was significantly lower than that of MS+TH. After 180 d of cultivation, total organic carbon content of all treatments with straw addition was significantly higher by 7.47% to 10.97% compared to CK. Moreover, organic carbon content of macroaggregates in TH+FP and all treatments with straw addition(except for MS+TH+FP), was significantly higher by 4.65% to 11.83% compared to CK. Aggregate stability showed a significant positive correlation with content of total organic carbon and organic carbon in different levels of aggregates, contributions of organic carbon in macroaggregates to total organic carbon content, and a significant negative correlation with the contribution of organic carbon in microaggregates and clay and silt to total organic carbon content. Redundancy analysis indicated that organic carbon had a significant impact on the size distribution and stability of aggregates. After 180 d of cultivation, FP and MS+TH exhibited significantly higher aggregate stability compared to other treatments, showing increases of 16.55% and 15.25% respectively, compared to CK. These treatments are therefore preferred options for improving the aggregate structure of heavy clay soil.