In this paper, we present a simulation study on clocking misalignment tolerance of pipelined magnetic quantum-dot cellular automata (MQCA) architectures. By the three-phase pipelined clocking and deduced clocking misalignment model, a systematic evaluation of impacts of clocking misalignment on four fundamental MQCA architectures is performed at non-zero temperatures. It is found that for the fixed nanomagnet size, majority logic gate is the most reliable structure, while the corner is most susceptible to clocking misalignment. High temperature gives rise to a negative effect on allowable misalignment angles. The results also show that as the aspect ratio of nanomagnet increases, the ability that all the MQCA architectures tolerate clocking misalignment decreases. Moreover, we analyze potential reason of pipelined MQCA architecture failures by examining the energy profile of neighboring zone nanomagnets and conclude that various energy barrier difference accounts for failure of MQCA architectures under clocking misalignment defect.