We present a theoretical study of the finite-temperature Kosterlitz-Thouless (KT) and vortex-antivortex lattice (VAL) melting transitions in two-dimensional Fermi gases with p-or d-wave pairing. For both pairings, when the interaction is tuned from weak to strong attractions, we observe a quantum phase transition from the Bardeen-Cooper-Schrieffer (BCS) superfluidity to the Bose-Einstein condensation (BEC) of difermions. The KT and VAL transition temperatures increase during this BCS-BEC transition and approach constant values in the deep BEC region. The BCS-BEC transition is characterized by the non-analyticities of the chemical potential, the superfluid order parameter, and the sound velocities as functions of the interaction strength at both zero and finite temperatures; however, the temperature effect tends to weaken the non-analyticities comparing to the zero temperature case. The effect of mismatched Fermi surfaces on the d-wave pairing is also studied.