In recent years, the source localization technique of magnetoencephalography (MEG) has played a prominent role in cognitive neuroscience and in the diagnosis and treatment of neurological and psychological disorders. However, locating deep brain activities such as in the mesial temporal structures, especially in preoperative evaluation of epilepsy patients, may be more challenging. In this work we have proposed a modified beamforming approach for finding deep sources. First, an iterative spatiotemporal signal decomposition was employed for reconstructing the sensor arrays, which could characterize the intrinsic discriminant features for interpreting sensor signals. Next, a sensor covariance matrix was estimated under the new reconstructed space. Then, a well-known vector beamforming approach, which was a linearly constraint minimum variance (LCMV) approach, was applied to compute the solution for the inverse problem. It can be shown that the proposed source localization approach can give better localization accuracy than two other commonly-used beamforming methods (LCMV, MUSIC) in simulated MEG measurements generated with deep sources. Further, we applied the proposed approach to real MEG data recorded from ten patients with medically-refractory mesial temporal lobe epilepsy (mTLE) for finding epileptogenic zone(s), and there was a good agreement between those findings by the proposed approach and the clinical comprehensive results.