A microlens array-based ultrathin microscope is provided. The microlens array-based ultrathin microscope includes a filter unit configured to selectively transmit fluorescence manifested in a measurement sample, and an image unit configured to acquire an image from light transmitted by the filter unit. The filter unit is formed to be in contact with or spaced apart from one surface of a transparent substrate, and the image unit includes a microlens array formed on an opposite surface to the transparent substrate in which the filter unit is formed, and an image sensor configured to collect image information of the microlens array.