For the three dimensional linearized MHD boundary layer system around a shear flow, we establish a well-posedness result with Sobolev regularity in one tangential direction under the non-degeneracy condition in that direction. The proof is based on an observation of a new cancellation mechanism that is different from the two space dimensional case. Precisely, the new cancellation relies on the evolution of the magnetic field orthogonal to the boundary instead of the stream function in two space dimension. Even though this kind of cancellation can help to lower the regularity requirement in only one tangential direction while analyticity is still needed in the other tangential direction, we expect that this can be viewed as one step further to study the challenging problem on the well-posedness theory in Sobolev space of the three dimensional MHD boundary layer system under some suitable structural assumption.