Fluorescence molecular tomography is a robust molecular imaging technology with low side effects which is a very hot topic in photobiology always. The fluorescence molecular tomography has better reconstruction results generally, if the excitation plane is close to the fluorescent targets. To find better excitation planes, we propose a location method of excitation planes based on mixture Gaussian distribution. Firstly, the method uses several excitation sources to obtain the living organism external surface distribution of the emitting light. Secondly, the Gaussian mixture model with pruning strategy is used to fit the distribution. Finally, the number and locations of the excitation planes are automatically determined according to fitted peak values. Fluorescence molecular tomography inverse problems are built based on the excitation light source of new excitation planes, and fluorescent targets are reconstructed using the inverse problems. Experimental results demonstrate that the fluorescence molecular tomography reconstruction results depending on the new excitation planes are much better than the results depending on original excitation planes.