Abstract Soil ciliates have advantages in monitoring soil quality after pollution and disturbance. However the potential is limited by the shortcoming of integrating quantitative and qualitative techniques. Here we utilized the Ludox-Quantitative Protargol Stain (Ludox-QPS) method which was originally developed for marine sediment to assess ciliate diversity in soil. The method was tested with three soil samples and compared with a ciliate-specific Denaturing Gradient Gel Electrophoresis (DGGE) and direct count method. The Ludox-QPS method obtained significantly higher number of ciliates with higher taxonomic resolution than the direct count, and revealed higher diversity than the DGGE as well as subsequent gene sequencing. Besides, we evaluated the effects of 2% glutaraldehyde fixative and the QPS preparation on cell size of one species from each of the three dominant ciliate assemblages in soil: colpodids, hypotrichs and haptorids. The experiment indicates a biovolume conversion factor of ∼0.69 for soil ciliates treated with the Ludox-QPS method. The Ludox-QPS method fulfills the enumeration of soil ciliates with good taxonomic resolution and thus promotes the utilization of ciliates in the bioassessment of soil environments.