Objective: To study the domain influencing factors and their internal relations which exist in hospitalization expenses of the main systematic diseases in rural health institutions in Nantong, to explore the main causes of unreasonable expenses growth, and put forward some suggestions. Methods: Factor analysis method was used to analyze the various indicators of hospitalization expenses among the illness case first pages of rural second-level hospitals and first-level health services centers in Haian and Haimen in April 2005. Results: Factors of examination fee and laboratory fee, treatment fee and nursing fee, bed fee and check fee, other fee, were the four public factors influencing hospitalization expenses. Conclusion: Make clear correlation and characteristics of public factors, take comprehensive measures to control unreasonable rise in hospitalization expenses in rural area.