Fluorescence molecular tomography (FMT), as a powerful imaging technique in preclinical research, can offer the three-dimensional distribution of biomarkers by detecting the fluorescently labelled probe noninvasively. However, because of the light scattering effect and the ill-pose of inverse problem, it is challenging to develop an efficient reconstruction method, which can provide accurate location and morphology of the fluorescence distribution. In this research, we proposed a novel adaptive Gaussian weighted Laplace prior (AGWLP) regularization method, which assumed the variance of fluorescence intensity between any two voxels had a non-linear correlation with their Gaussian distance. It utilized an adaptive Gaussian kernel parameter strategy to achieve accurate morphological reconstructions in FMT. To evaluate the performance of AGWLP method, we conducted numerical simulation and in vivo experiments. The results were compared with fast iterative shrinkage (FIS) thresholding method, Split Bregman-resolved TV (SBRTV) regularization method and Gaussian weighted Laplace prior (GWLP) regularization method. We validated in vivo imaging results against planar fluorescence images of frozen sections. The results demonstrated that AGWLP method achieved superior performance in both location and shape recovery of fluorescence distribution. This enabled FMT more suitable and practical for in vivo visualization of biomarkers.