Horizontal well is an important way to develop thin reservoir with edge-bottom water aquifer. For the horizontal well near oil–water contact, the reservoir have the features of edge water and bottom water at the same time. The productivity formula of horizontal well in pure edge water or pure bottom water reservoir is not fully applicable to this type of reservoir. For the heterogeneous reservoir with composite water aquifer, the horizontal well is divided into multiple well sections by using the concept of multi-segment well. Based on the seepage mechanics theory and potential superposition principle, considering the mutual interference between multi well sections, the productivity formula of horizontal well in heterogeneous reservoir with composite water aquifer is established. The new productivity formula considers the effect of reservoir heterogeneity, the quasi-linear flow of lateral edge water and the ellipsoidal flow of vertical bottom water. It can effectively determine the influence range and drainage distance of edge water in a heterogeneous reservoir with composite water aquifer. According to the test data of horizontal wells in Weizhou 11-1 oilfield, the drainage distance b of edge water is fitted and used to predict the productivity of new wells, and the result is very good. The research result lays a foundation for productivity prediction of horizontal well in heterogeneous reservoir with composite water aquifer.