Long-term chemical fertilization (especially nitrogen fertilization) under intensive land-management practices in agriculture is of great concern globally due to its adverse influence on the environment and human health. Returning the eco-friendly crop residues to farmland is a promising way of reducing chemical fertilizer input and alleviating environmental problems.【Objective】 Protists are unicellular eukaryotes with enormous abundance and diversity, and play versatile functional roles to improve soil fertility and agricultural productivity. Thus, they comprise an integral component of soil microbiota in the agroecosystem. However, little is known about the responses of the soil protist community to nitrogen fertilization in combination with straw incorporation.【Method】 Here, a fixed field trial with 2×4 full-factor interaction was performed to examine the variations in diversity, composition, and potential function of the protistan community using Illumina high-throughput sequencing under eight different fertilization treatments (2 straw returning groups×4 nitrogen gradients), Also, the key forces driving the variation in soil protistan community were determined in combination with edaphic property analysis.【Result】 The phyla Chlorophyta, Conosa, Cercozoa and Ciliophora were dominant in the soils for all treatments. Nitrogen fertilization diminished the diversity of soil protists, whereas straw returning in general modified such impacts, with more pronounced effects under higher nitrogen application rates. Regardless of whether straw was added, the relative abundance of Chlorophyta exhibited an overall decrease with increased nitrogen gradient. Cercozoa and Ciliophora presented an increase in proportion with the amount of nitrogen fertilizer in the straw returning group. In the current study, the protistan functional community was predominated by phagotrophs in all treatments. Compared to treatments without straw addition, the implementation of straw returning enhanced the relative abundance of phagotrophs, but suppressed the proportion of phototrophs. Protistan parasites preferred a high nitrogen input under exclusive nitrogen fertilizer, with highest proportion in N300 treatment, which was significantly higher than those in all other treatments. Soil properties were important environmental factors determining the shifts in soil protist community, with soil organic matter and pH exhibiting the most intensive influences as revealed by redundancy analysis (RDA) and Pearson’s correlation analysis.【Conclusion】 This study provides experimental evidence that nitrogen fertilization coupled with straw incorporation have consequences for the soil protist community. It also shows that the phylogenetic and functional taxa of protists are responsive to such agricultural management regime alterations. Future studies should aim at deciphering the trophic associations among microorganisms, as well as constructing agricultural soil microhabitat beneficial for crops based on reasonable fertilization regimes and utilization of biotic resources like protists.