To investigate the effects of catch crops as a substitute for organic fertilizer on soil protist communities in greenhouse facilities, this study conducted a randomized block field experiment with five treatments that is conventional organic fertilizer application with fallow (CK), 50% conventional organic fertilizer with fallow (NC), 50% conventional organic fertilizer with forage maize (CM), forage sorghum (CS), and forage legumes (CL) during the fallow season. Amplicon sequencing was used to analyze changes in protist communities. Results showed that protist communities in all treatments were dominated by the Amoebozoa (46.9%) and SAR (45.1%) supergroups. CS and CL treatments significantly increased the Shannon diversity index by 26.1% and 22.9%, respectively (P < 0.05). Functional composition analysis revealed that predatory protists were predominant (59.1%-65.0%), with cover crop treatments increasing their relative abundance by 3.9%-10.0% and decreasing phototrophic protists by 7.2%-42.2% (P < 0.05). The correlation matrix between soil protist species composition and soil physicochemical properties, along with partial least squares path modeling, demonstrated that soil properties (available potassium and organic matter) had negative effects on phototrophic protists (P < 0.001) and positive effects on predatory protists, with predatory protists contributing most to community diversity. Cover crops can regulate the functional group structure of soil protists and enhance soil protist diversity by improving soil physicochemical properties, providing a scientific basis for sustainable management of greenhouse soils.