Due to the limitations that the current interwell connectivity can not consider shut-in wells and the inversion solving method is not reliable, a novel model that can consider the compressibility and shut-in situations is established. In order to further decrease the ill-posedness of the solutions for the connectivity model, a constraint optimization algorithm by using Bayesian theories and projection gradient method are proposed. The tests for a synthetic reservoir model and a real oil field indicate that the proposed methodology can efficiently estimate the interwell connectivity with high precision and reliability for practical application.