We report a new microfabrication method of multifocal microlens arrays (MF-MLAs) for extended depth-of-field (DoF) using multilayer photolithography and thermal reflow. Microlenses of different focal lengths were simultaneously fabricated on a single glass wafer by using repeated photolithography with multiple photomasks to define microposts of different thicknesses and concurrent thermal reflow of multi-stacked microposts. The diverse lens curvatures of MF-MLAs are precisely controlled by the thickness of the micropost. Hexagonally packaged MF-MLAs clearly show three different focal lengths of 249 µm, 310 µm, and 460 µm for 200 µm in lens diameter and result in multifocal images on a single image sensor. This method provides a new route for developing various three-dimensional (3D) imaging applications such as light-field cameras or 3D medical endoscopes.