Three-dimensional (3D) cell cultures have contributed to a variety of biological research fields by filling the gap between monolayers and animal models. The modern optical sectioning microscopic methods make it possible to probe the complexity of 3D cell cultures but are limited by the inherent opaqueness. While tissue optical clearing methods have emerged as powerful tools for investigating whole-mount tissues in 3D, they often have limitations, such as being too harsh for fragile 3D cell cultures, requiring complex handling protocols, or inducing tissue deformation with shrinkage or expansion. To address this issue, we proposed a modified optical clearing method for 3D cell cultures, called MACS-W, which is simple, highly efficient, and morphology-preserving. In our evaluation of MACS-W, we found that it exhibits excellent clearing capability in just 10$$min, with minimal deformation, and helps drug evaluation on tumor spheroids. In summary, MACS-W is a fast, minimally-deformative and fluorescence compatible clearing method that has the potential to be widely used in the studies of 3D cell cultures.