Background Immune cells are important for the development of schistosomiasis japonica and are also critical for the treatment of schistosomiasis. The immune cells in the peripheral blood help assess the immune state. The peripheral lymphocytes in schistosomiasis mansoni were well studied, however immune cells in patients with different stages of Schistosomiasis Japonica are not well analyzed. Here we performed a preliminary study to explore characteristics of peripheral lymphocyte subsets in patients with different stages of Schistosomiasis Japonica. Methods 135 patients with S. japonicum infection and 25 healthy volunteers were included in this study, including 84 patients with chronic S. japonicum infection and 51 patients with advanced S. japonicum infection. Flow cytometry analysis was performed to evaluate peripheral lymphocytes including T cells, B cells and NK cells. Blood routine and liver function test data were analyzed. Ultrasound examination was used to access liver fibrosis according to the World Health Organization standard about ultrasound in schistosomiasis. Results Demographic data analysis suggested there was no difference in age and gender in patients with S. japonicum infection and health control group. Liver function tests showed that patients with advanced schistosomiasis had a higher incidence of liver function abnormality and blood lipid than those with chronic schistosomiasis. Blood routine results reflected that hemoglobin, red blood cells, platelets, as well as lymphocytes in the advanced group were significantly less than that in the chronic group. Furthermore, flow cytometry analysis indicated that the percentage of CD4 ⁺T cells was lower in the advanced group, but the percentage of CD19 ⁺B cells was higher in the advanced group. In addition, the number of CD3 ⁺T cells, CD3 ⁺CD4 ⁺T cells, CD3 ⁺CD8 ⁺T cells, and NK cells was less in the advanced group when compared with those in the chronic group. In addition, there was a correlation between the decrease in CD4 ⁺ T cells and more severe fibrosis on ultrasound images. Conclusion Our results indicated that the immune state in the peripheral is different in different stages of S. japonicum infection. Lymphocyte subset analysis have potential to facilitate differential diagnosis of different stages of schistosomiasis japonica and even to be a prognostic factor.