To investigate the effects of catch crops as the substitutes for organic fertilizers on soil protist communities in greenhouse facilities, a randomized block field experiment was conducted with five treatments: 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 Amoebozoa (46.9%) and SAR (45.1%) supergroups. CS and CL significantly increased Shannon diversity index of protist communities by 26.1% and 22.9%, respectively (P<0.05). Functional composition analysis revealed that predatory protists were predominant (59.1%-65.0%), and the catch cropping treatments increased their relative abundance by 3.9%-10.0%; while the relative abundance of phototrophic protists decreased by 7.2%-42.2%, with a significant decrease under the CS treatment(P<0.05). The correlation analysis 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 a significant negative effect on phototrophic protists (P<0.001), and a positive but not significant effect on predatory protists, with predatory protists contributing most to community diversity. In conclusion, catch crops can regulate the functional group structure of soil protists and enhance soil protist diversity by improving soil physicochemical properties. The study provided a scientific basis for sustainable management of greenhouse soils.