Considering the operation effect, safety, support security and environmental friendliness of waterways as the main evaluation factors, an evaluation index system for healthy development of regional inland waterway including 14 evaluation indices is established. Based on the statistical data of inland waterways in Suqian City in 2014, the healthy development degree of the inland waterways is computed by using the method of variable fuzzy sets. The results show the healthy development level of the inland waterways in Suqian City is the same under different parameter combinations. The 14 evaluation indices can be divided into three types. The evaluated results basically reflect the actual situations of the inland waterways in Suqian City. It is indicated that the proposed evaluation system and the theory of variable fuzzy sets can be employed to evaluate the healthy development level of regional inland waterways.