In this paper, a novel medium access control (MAC) layer protocol is introduced for unmanned aerial vehicle (UAV)-based mission critical wireless sensor networks (MC-WSN), which is an important application of mission critical sensor and sensor networks (MC-SSN). The UAVs hovering in the threedimensional monitoring networks are distributed in subsets according to their distance from the center station. UAVs in the same subset are contending for access and transmission, while each subset is allotted a slot based on adaptive time division multiple access (TDMA) scheme. As a multi-channel system, a novel channel allocation algorithm is presented for subset relay transmission period to optimize the performance of networks. The UAV returning period for charging is utilized in the protocol to enhance the transmission throughput and mitigate delay. Detection slot and position prediction algorithm are designed in the UAV returning period to improve the throughput and reduce the delay. The simulation results verify the improvement on throughput and delays of the proposed protocol for UAV-based MC-WSN. INDEX TERMS Mission-critical wireless sensor networks, UAVs monitoring system, media access control protocol, channel allocation.