Adaptive finite element method (AFEM) is broadly adopted to recover the internal source in biological tissues. In this letter, a novel dual-mesh alternation strategy (dual-mesh AFEM) is developed for bioluminescence tomography. By comprehensively considering the error estimation of the finite element method solution on each mesh, two different adaptive strategies based on the error indicator of the reconstructed source and the photon flux density are used alternately in the process. Combined with the constantly adjusted permissible region in the adaptive process, the new algorithm can achieve a more accurate source location compared with the AFEM in the previous experiments.