A time-of-flight (TOF) based mass microscope system for an ultra-high speed multi-mode mass analysis, the time-of-flight based mass microscope system performing a mass imaging analysis of a sample in a microscope mode by irradiating a laser beam, an ion beam, or any one of the laser beam and the ion beam in a defocused state on the sample, photographing an image of the sample, and simultaneously measuring and detecting a position of a secondary ion generated from the sample at the time of irradiating the laser beam or the ion beam, based on a time-of-flight (TOF), so as to perform the analysis with respect to all samples having from a low molecular weight sample to a high molecular weight sample.