Optical microscopy plays a critical role in the fabrication of two-dimensional (2D) van der Waals heterostructures. An outstanding challenge in conventional microscopy is to visualize transparent 2D layers as well as embedded monolayers in a stacked heterostructure with high optical contrast. Phase-contrast microscopy, first developed by Frits Zernike in the 1930s, leverages the interference effect between specimen scattered light and background light to increase the contrast of transparent specimens. Such phase-contrast microscopy, always in a transmission configuration, revolutionized the study of transparent cellular structures in biology. Here, we develop a versatile reflective phase-contrast microscopy for imaging 2D heterostructures. We employ two spatial light modulators to flexibly control the intensity and phase of the illumination and the reflected light. This reflective phase-contrast microscopy achieves unprecedented high contrast for imaging a transparent 2D monolayer. It also enables direct observation of 2D monolayers embedded inside a thick heterostructure that are “invisible” in conventional microscopy.