Objective To examine the effect of mouse splenic granulomas on the structure and function of splenic lymphoid follicles at a late stage of Schistosoma japonicum infectio. Methods Fifteen C57BL/6 mice were infected with 20 S. japonicum cercariaes each via abdominal skin. Mice were sacrificed 16 weeks post-infection for spleen sampling, and divided into two groups presence of egg granulomas on the spleen surface, including the splenic granuloma group and non-granuloma group, while mice 5 weeks post-infection (8 mice) and healthy mice (7 mice) served as infection and healthy controls. The spleens of mice in each group were weighed and splenic lymphocytes were collected, and the structure of mouse splenic lymphoid follicles was observed using HE staining. The distribution of positive mucosal addressin cell adhesion molecule-1 (MAdCAM-1⁺) cells was observed in the marginal zone of lymphoid follicles using indirect immunofluorescence, and the distribution of Ki67⁺ and PNA⁺ germinal center cells was observed in mouse spleens using immunohistochemical and direct immunofluorescence. Mouse splenic CD4⁺ T cells were isolated with magnetic beads, and the proportion of follicular helper T (Tfh) cells in mouse splenic CD4⁺ T cells was detected using flow cytometry. Results More severe splenomegaly was seen in mice infected with S. japonicum for 16 weeks in relative to mice infected with S. japonicum for 5 weeks and healthy mice, and the mousse spleen weight was significantly lower in the splenic granuloma group (0.37 ± 0.04) than in the non-granuloma group (0.48 ± 0.04) (F = 266.17, P < 0.01). HE and indirect immunofluorescence revealed a decrease in the number of splenic lymphoid follicles, follicle areas, counts of MAdCAM-1⁺ cells in the marginal zone in the splenic granuloma group, while no lymphoid follicles or their marginal zone structures were detected in the non-granuloma group. Immunohistochemical and direct immunofluorescence demonstrated decreased numbers of Ki67⁺ and PNA⁺ germinal center cells in the splenic granuloma group compared with healthy controls, while no Ki67⁺ or PNA⁺ germinal center cells were observed in the non-granuloma group. Flow cytometry detected that the proportion of positive inducible costimulator (ICOS⁺) and chemokine C-X-C motif receptor 5 (CXCR5⁺) Tfh cells was significantly higher in mouse splenic CD4⁺ T cells in the splenic granuloma group [(0.54 ± 0.06)%] than in the non-granuloma group [(0.36 ± 0.05)%] (F = 61.68, P < 0.01）, and the proportion of ICOS⁺ positive programmed cell death protein 1 (PD1⁺) Tfh cells was significantly higher in mouse splenic CD4⁺ T cells in the splenic granuloma group [(5.25 ± 0.17)%] than in the non-granuloma group [(2.40 ± 0.09)%] (F = 29.13, P < 0.01), and the proportion of ICOS⁺CXCR5⁺PD1⁺ Tfh cells was higher in the splenic granuloma group [(0.42 ± 0.06)%] than in the non-granulomas group [(0.26 ± 0.05)%] (F = 20.03, P < 0.01）. Conclusion Alleviated splenic pathological damages and more intact internal functional structures that generate antibodies, such as germinal center and follicles, are seen in mice with splenic granulomas than in those without granulomas at a late stage of S. japonicum infection, which may result in a higher antibody level in mice with splenic granulomas than in those without granulomas at a late stage of S. japonicum infection.