With the rapid economic increase, the transboundary watershed pollution has become very seriously. From the practical experience of solving this problem in foreign countries, the control of pollutants emission by cooperation of different regions is an economic way to solve the problem. According to the current international and domestic researches, most studies were limited to analyze the benefit allocation in fully cooperative coalition while ignored the acceptability and stabilization of the benefit allocation of the cooperative groups. Based on this shortage, this paper established a cooperative game model of solving the transboundary watershed pollution problem. We used this model to analyze the Jialu River watershed whose area includes the regions of Zhengzhou, Kaifeng, Xuchang and Luohe. From the perspective of game theory, we used four different benefit allocation schemes to analyze the possibility and stabilization in different cooperative groups for these regions. The results showed that the benefit allocations of Shapley value and SCRB (Separable Cost Remaining Benefit) method have better acceptability and stabilization than the rest of methods. If we use the Shapley value to allocated benefits which formed in fully cooperative coalition, Zhengzhou, Kaifeng, Xuchang and Luohe can acquire benefit about 391.22×104, 100.55×104, 76.3×104 and 269.35×104 yuan, respectively. And if we use the SCRB method to allocate that benefits, then Zhengzhou, Kaifeng, Xuchang and Luohe can acquire benefit about 400.94×104, 96.06×104, 74.35×104 and 266.06×104 yuan, respectively. Despite the higher likelihood of Shapley value and SCRB method to be accepted by these regions, the stabilizations of the two methods were not good enough. The benefit allocation result of Shapley value showed that the stabilization of Zhengzhou, Kaifeng, Xuchang and Luohe was 0.95, 0.82, 0.86 and 0.88, respectively. Meanwhile, the result of SCRB method was that the stabilization of Zhengzhou, Kaifeng, Xuchang and Luohe was 0.9, 0.9, 0.9 and 0.9, respectively. The two results indicated that the voluntary negotiation on forming fully cooperative coalition in these study regions was not sustainable.