The uplink of navigation data as satellite ephemeris is a complex satellite range scheduling problem. Large-scale optimal problems cannot be tackled using traditional heuristic methods, and the efficiency of standard genetic algorithm is unsatisfactory. We propose a multi-objective immune genetic algorithm (IGA) for uplink scheduling of navigation constellation. The method focuses on balance traffic and maximum task objects based on satellite-ground index encoding method, individual diversity evaluation and memory library. Numerical results show that the multi-hierarchical encoding method can improve the computation efficiency, the fuzzy deviation toleration method can speed up convergence, and the method can achieve the balance target with a negligible loss in task number (approximately 2.98%). The proposed algorithm is a general method and thus can be used in similar problems.