Joint distribution alliance constructed by urban logistics enterprises usually adopts horizontal logistics cooperation, and sub-alliances are often formed under this mode. In order to solve the profit allocation problem of the joint distribution alliance with sub-alliance, the contribution excess of sub-alliance is introduced, and the quadratic programming model which minimizes the overall dissatisfaction of the alliance is constructed based on this model. The least squares solution considering the contribution of sub-alliance is obtained, which is proved to be effective, unique and additive. Finally, cost accounting is conducted for urban logistics enterprises, and the rationality and practicability of the strategy is verified by the case of joint distribution alliance. It can be seen that the profit allocation strategy considering the contribution of sub-alliance can effectively solve the problem of profit allocation of joint distribution alliance and ensure that all parties in the alliance can obtain satisfactory profits.