With the rapid increase of mission demands for the tracking and data relay satellite system (TDRSS), the technical issue of high-efficient scheduling has attracted more attention in recent years. Most of previous scheduling algorithms are designed based on the assumption of missions' uniform time- space distribution, which have showed unsatisfactory performance in real scenarios with non-uniform distribution of mission demands. In this paper, we first transform the TDRSS scheduling problem into the heterogeneous inter- satellite link antenna (ILA) pointing route problem. Then, a two-stage heuristic algorithm with hierarchical scheduling strategies is proposed with the consideration of non-uniform time-space distribution of missions. Finally, we employ the TDRSS dataset to verify our proposed algorithm by comparing with the improved Rojanasoonthon's greedy randomized adaptive search procedure (GRASP) algorithm. Experimental results show that our proposed two-stage heuristic algorithm can schedule 2.41%, 4.43% and 6.02% more missions and consume 11.84%, 10.38% and 9.54% less setup times of SA antennas than the improved GRASP algorithm for the mission scale of 200, 400 and 600, respectively. In addition, setup times of SA antennas in those instances with non-uniform distribution in space can be more efficiently compressed by our proposed two-stage heuristic algorithm.