In this paper, we develop and analyze an adaptive multiscale approach for heterogeneous problems in perforated domains. We consider commonly used model problems including the Laplace equation, the elasticity equation, and the Stokes system in perforated regions. In many applications, these problems have a multiscale nature arising because of the perforations, their geometries, the sizes of the perforations, and configurations. Typical modeling approaches extract average properties in each coarse region, that encapsulate many perforations, and formulate a coarse-grid problem. In some applications, the coarse-grid problem can have a different form from the fine-scale problem, e.g. the coarse-grid system corresponding to a Stokes system in perforated domains leads to Darcy equations on a coarse grid. In this paper, we present a general offline/online procedure, which can adequately and adaptively