Rapid economic development in many countries is leading to global environmental degradation. Consequently, the restoration of degraded ecosystems has become an important component of modern ecological research. In the 1990s, China started the key project of returning farmland to forest in order to realize ecological restoration benefits. Benefits of ecological restoration include protecting and improving the environment and minimizing soil erosion, mitigating the threat of floods, and enhancing biodiversity. With the implementation of the project of returning farmland to forest, studies on returning farmland to forest (grass) have gradually increased, but there has been more emphasis on returning farmland to forests, ecological benefits, vegetation, and the soil environment. Microorganisms play a key role in driving biogeochemical cycles in ecosystems. However, knowledge of soil microbial communities is poor. It is therefore becoming increasingly important to gain a better understanding of soil microorganisms including microbial eukaryotes (protists). Ciliated protists (ciliates) play an important role in microbial food webs, controlling bacterial populations by predation, transferring carbon and energy through food chains, and releasing nutrients. In soils, the presence of ciliates and other heterotrophic protists is known to significantly increase levels of available plant nutrients, such as nitrogen and phosphorous. Furthermore, because of their rich species, short growth cycles, rapid community evolution and sensitivity to environmental change, they are often used as indicators of environmental quality. Current research on soil ciliates mainly focuses on classification, morphogenesis, and molecular information. Changes of soil ciliate community structure after returning farmland to forest and the use of ciliate community structure for evaluating environmental change have received only scant attention.This study investigates the response of soil ciliate communities to the ecological restoration of three different forest types in this region including A1 (Picea asperata×Hippophae rhamnoides), A2 (Picea asperata), and B1 (Hippophae rhamnoides). These forests had previously been destroyed for the growth of agricultural crops. Soil samples were collected from each of the three forest types and from two crops (A0:Triticum aestivum, B0:Pisum sativum) as controls. Ciliates were isolated from the samples using the non-flooded Petri dish method. Ciliate communities were characterized by observation of cells in vivo using light microscopy. Enumeration was by directing-culture counting. Physical-chemical parameters also were recorded. The main aim of the study was to relate soil ciliate community characteristics with vegetation and environmental factors under different restoration patterns. A total of 125 species belonging to 9 classes, 19 orders, 29 families, and 34 genera of ciliates were recorded. Significant differences in the community structure of soil ciliates (P < 0.05) were found between the restored forest soils and the control soils. The species richness, density, species diversity index, evenness index, and abundance index of soil ciliates were all significantly higher (P < 0.05) in the restored forest soils than in the soils from the control cultivars, which from high to low were A1 > B1 > A2 > B0 > A0. Furthermore, the dominant ciliate group in control soils (order Colpodida) was replaced by the order Sporadotrichida in the restored forest soils. Results of correlation analysis and redundancy analysis were similar with both showing that soil water content, organic matter and total nitrogen content were the main factors influencing the ciliate community structure in the restored forest soils.