The application of chemical fertilizer alone may deteriorate the trophic structure of soil nematode community. However, little is known about whether the combined application of organic materials and chemical fertilizer can mitigate the negative effect, and the mechanism that potentially mitigates the negative effect remains poorly understood. In this study, four fertilization regimes, including unfertilized control (CK), chemical nitrogen (N), phosphorus (P) and potassium (K) fertilizer (NPK), crop straw combined with NPK (SNPK), and pig manure combined with NPK (MNPK), were used to determine the variations in soil nematode trophic groups, diversity, and functional indices under different fertilization regimes. Results indicate that NPK treatment significantly increased the abundances of both bacterivores and plant parasites, and the increase amplitude in the abundance of plant parasites was higher than that of bacterivores under the NPK treatment in comparison to the CK treatment, which might lead to the deterioration of the trophic structure of nematode community. By comparing the difference in the abundance of the plant-parasitic nematode genera among different fertilization regimes, it can be observed that the increase in the abundance of the plant-parasitic nematode-dominant genus Dolichorhynchus under the NPK treatment mainly contributed to the increase in the abundance of plant parasites and the subsequent deterioration of the trophic structure of nematode community. Compared to the NPK treatment, SNPK and MNPK treatments suppressed the increase in the abundance of the Dolichorhynchus, which will help to mitigate the negative effect of NPK treatment on the trophic structure of nematode community. Moreover, the significantly negative correlation of the Dolichorhynchus and soil total nitrogen (TN) indicates that the suppression of this nematode genus is under high N content. Overall, these results suggest that NPK treatment might deteriorate the trophic structure of nematode community mainly by increasing the abundance of the Dolichorhynchus, while the combined application of crop straw or pig manure and chemical fertilizer could mitigate the negative effect by suppressing the Dolichorhynchus with increasing N concentration, which may be more conducive to maintaining agricultural sustainability.