Inverse opal scaffolds have recently emerged as a novel class of scaffolds with uniform and controllable pore sizes for tissue engineering to provide better nutrient transport, a uniform cell distribution, and an adjustable microenvironment for cell differentiation. However, when the pore size of the scaffold is much larger than the dimension of a cell, the cell actually encounters a local 2D environment and the void space associated with the pore can not be efficiently utilized. Here, we demonstrate that a truly 3D microenvironment can be created inside a pore by further functionalizing the as-prepared inverse opal scaffold with a second polymer by freeze-drying. The resultant inverse opal scaffold with hierarchically structured pores can enhance both cell proliferation and tissue infiltration.