This study compared physicians' practices on three treatment procedures and hospitalization days with guideline recommendations to assess guideline adherence in the treatment of advanced schistosomiasis japonica. Descriptive statistics were used to estimate patients' characteristics and rate of guideline adherence. And chi-square tests were used to assess influences of severity of the disease on guideline adherence. The study found no one (0/173) adhered to adequate diagnosis, treatment regimens, and discharge criteria of guidelines completely. And 2.23% of patients in group 1 and 4.23% in group 2 were totally conforming to adequate diagnosis. 91.91% of patients were conforming to adequate treatment regimens among which group 1 and group 2 were 90.32 and 92.25%, respectively. And one (2.23%) patient in group 1 and zero (0%) in group 2 were conforming to discharge criteria of guidelines, and most of the patients left hospital without symptom checks (151/173), liver function and biochemical tests (169/173), and complication checks (91/173). Among 173 inpatients, rate of adequate hospitalization days was 36.42% (63/173). And chi-square test suggested no significant difference (P > 0.05) on guideline adherence in two groups, which implied both of critical and general patients' treatments should be stressed to comply with guidelines. There existed a large gap between guidelines and practices of the treatment of advanced schistosomiasis japonica.