Objective To explore the potential therapeutic effect of Schistosoma japonicum soluble worm protein (SjSWP) and recombinant cystatin (rSjcystatin) on 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis in a mouse model that mimics human inflammatory bowel diseases(IBDs). Methods Twenty-four female BALB/c mice were divided into four groups: non-treated control group(control), phosphate buffer (PBS) treated group, rSjcystatin treated group (rSjcystatin) and SjSWP treated group(SjSWP). The PBS, rSjcystatin, SjSWP treated groups were respectively intraperitoneally injected with 100 μl PBS, 50 μg rSjcystatin and 50 μg SjSWP at 6 h and 24 h after being induced with 0.1 ml of 5% TNBS by enema for colitis, while the control group was injected with the same amount of PBS at corresponding time without colitis induced. After 72 hours of TNBS enema, mice in each group were sacrificed under anesthesia. The pathological and inflammatory parameters were determined by measuring macroscopic score, myeloperoxidase (MPO) activity, colon length and microscopic score. The Th1 to Th2 cells and T regulatory cells (Tregs) in the spleen of mice were measured by flow cytometry, and the immune responses induced by rSjcystatin and SjSWP were investigated. The levels of cytokines including interferon-gamma (IFN-γ), interleukin-4 (IL-4), IL-13, IL-10 in the colon tissue of mice were detected by enzyme-linked immunosorbent assay (ELISA). Multiple groups of measurement data were analyzed by one-way analysis of variance, and pairwise comparisons between multiple groups of mean were tested by Student-Newman-Keuls. Results The mice with TNBS-induced colitis showed significant inflammation and pathology characterized by the weight loss, rectal bleeding, diarrhea, colon shrinking and ulceration, as well as induced inflammatory cytokine INF-γ, inflammatory cell infiltration and increased MPO activity. In this study we identified that treatment with rSjcystatin and SjSWP significantly reduced the TNBS-induced colon inflammation characterized by reduced disease manifestations in macroscopic score (improved colon erosion, adhesion, ulceration and colon shrinking) and microscopic scores (less tissue damage and inflammation), compared to the group of mice received PBS only. The macroscopic scores of colon in the control group, PBS group, rSjcystatin group and SjSWP group were 0, 9.8 ± 0.8, 4.3 ± 1.0 and 4.5 ± 1.4; the mean microscopic scores of mice were 0, 6.00 ± 0.4, 2.2 ± 0.5 and 2.8 ± 0.6, respectively. Among the above results, rSjcystatin and SjSWP had significant differences compared with PBS group (F = 57.8, 34.1, P < 0.01). There was no significant difference between rSjcystatin group and SjSWP group（P > 0.05）. MPO values in control group, PBS group, rSjcystatin group and SjSWP group were (0.3 ± 0.0), (1.4 ± 0.1), (0.6 ± 0.1) and （0.6 ± 0.1）（F = 32.5, P < 0.01）; the Tregs in spleen were (4.4 ± 0.7), (8.2 ± 3.1), (18.4 ± 2.1) and (13.4 ± 1.9)% （F = 8.3, P < 0.01); the IFN-γ and IL-10 in colon tissue homogenate supernatants of colon tissue were (952.0 ± 61.1), (1 684.6 ± 158.3), (1 092.0 ± 81.9) and (1 001.6 ± 111.2) pg/ml; (322.8 ± 27.4), (399.3 ± 77.9), (860.6 ± 153.6) and (892.0 ± 113.8) pg/ml respectively （F = 9.6, 8.3, P < 0.05). The results showed that, in rSjcystatin group and SjSWP group, the inflammatory cytokine INF-γ, MPO activity in colon tissue decreased, combined with boosted Tregs response and the secretion of regulatory cytokine IL-10, compared to the group of mice received PBS only with statistical difference (P < 0.01). There was no significant difference for the therapeutic efficacy on inflammatory colitis between rSjcystatin group and SjSWP group(P > 0.05). Conclusions SjSWP and rSjcystatin could alleviate experimental colitis in mice via stimulating Tregs and Th2 mediated responses and, correspondingly, suppressing Th1 pro-inflammatory response related to the pathogenesis of colitis.