Aquifer connectivity could greatly affect groundwater flow and further control the contaminant transport in fractured medium. However, assessing connectivity of fractured aquifer at regional scales is still a challenge because such connectivity is difficult to measure directly. This study proposed a framework for assessing connectivity of a fractured aquifer, with Qitaihe area, Heilongjiang Province, northeastern China as an illustrating study area. The 3-D finite difference numerical models were established to interpret the results of three multi-well pumping tests and inversely estimate the distribution of hydraulic conductivity (K) in the fractured aquifer. A static connectivity metric of the minimum hydraulic resistance (MHR) was calculated, based on the optimized K-field, to evaluate the hydraulic connectivity in the aquifer, and the corresponding least resistance paths (LRPs) were identified. The results indicate that a better horizontal connectivity in the fractured aquifer in the northeastern and middle parts than in the southwestern part of the study area. The identified LRP indicated that the preferential flow channels at regional scales were controlled mainly by aquifer connectivity instead of local high-K zones.The results of this study can provide a method for aquifer connectivity estimation at regional scales.