Nematodes occupy different niches in soil and play important roles in plant growth. However, the dynamic responses of nematode community to fertilization at the aggregate scale and the relationships between key nematode indices and crop production are still unclear. A long-term field experiment with different fertilization regimes (CK, no fertilizer; NPK, synthetic fertilizers alone; BCNPK, biochar + synthetic fertilizers; OMNPK, pig manure + synthetic fertilizers; RSDNPK, crop straw + synthetic fertilizers) was conducted to link nematode and crop production. Higher total nematode abundance, biodiversity, and nematode metabolic footprint (NMF) were observed in the wheat season, while increased maturity index (MI), plant parasite index (PPI), and structure index (SI) were found in the maize season. The nematode community in the wheat season was more enriched and mature, especially in large macroaggregates. The composition of the nematode community was shifted by RSDNPK in both crop seasons, as indicated by the principal coordinates analysis (PCoA). Additionally, the 1.5-fold higher enrichment index (EI) under RSDNPK in comparison with other treatments in the wheat season also indicated a significantly differentiated nematode community. Compared with NPK, the wheat yield of RSDNPK (2265 kg ha(-1)) was 26 % lower, while the maize yield of this treatment (5776 kg ha(-1)) was >13 % higher. The PPI and SI in the seedling period of winter wheat and the PPI in the silking period as well as the variation of the nematode community in the maize season were key nematode indices that strongly correlated with the yields of corresponding crops. Crucial nematodes also exhibited notable positive or negative relationships with crop yields (P < 0.05). Overall, the combined application of synthetic fertilizers and crop straw can improve soil health through its positive effects on nematode community, which has the potential to propel crop production.