The main challenge of bioluminescence tomography (BLT) is the ill-posed, non-unique nature of the inverse problem. To get reliable reconstruction, permissible source region is a commonly used a priori knowledge in the inverse procedure. In this paper, to accurately reveal 3D distribution of bioluminescent sources from limited boundary measurement, we propose an iterative reconstruction method incorporating adaptive algebraic reconstruction technique (AART) and adaptively shrinking permissible source region. AART algorithm is applied to get the solution without permissible region. Base on the distribution of the solution, we calculate the expectation and the covariance matrix and then derive the parameters for determining a cuboid-shaped region. Simulation experiments on a 3D digital mouse and an in vivo experiment are conducted to validate the feasibility and evaluate the performance of the proposed reconstruction method. The reconstructed results demonstrate the shrinking strategy is helpful for improving the stability of inverse algorithm.