In light of the high bit error rate in satellite network links, the traditional transmission control protocol (TCP) fails to distinguish between congestion and wireless losses, and existing loss differentiation methods lack heterogeneous ensemble learning models, especially feature selection for loss differentiation, individual classifier selection methods, effective ensemble strategies, etc. A loss differentiation method based on heterogeneous ensemble learning (LDM-HEL) for low-Earth-orbit (LEO) satellite networks is proposed. This method utilizes the Relief and mutual information algorithms for selecting loss differentiation features and employs the least-squares support vector machine, decision tree, logistic regression, and K-nearest neighbor as individual learners. An ensemble strategy is designed using the stochastic gradient descent method to optimize the weights of individual learners. Simulation results demonstrate that the proposed LDM-HEL achieves higher accuracy rate, recall rate, and F1-score in the simulation scenario, and significantly improves throughput performance when applied to TCP. Compared with the integrated model LDM-satellite, the above indexes can be improved by 4.37%, 4.55%, 4.87%, and 9.28%, respectively.