This paper explores the application of the multiscale finite element method (MsFEM) to address steady-state Stokes-Darcy problems with BJS interface conditions in highly heterogeneous porous media. We assume the existence of multiscale features in the Darcy region and propose an algorithm for the multiscale Stokes-Darcy model. During the offline phase, we employ MsFEM to construct permeability-dependent offline bases for efficient coarse-grid simulation, with this process conducted in parallel to enhance its efficiency. In the online phase, we use the Robin-Robin algorithm to derive the model's solution. Subsequently, we conduct error analysis based on $L^2$ and $H^1$ norms, assuming certain periodic coefficients in the Darcy region. To validate our approach, we present extensive numerical tests on highly heterogeneous media, illustrating the results of the error analysis.