A novel multifocal multiphoton excited fluourescence microscopy (MMM) is presented. The required focus array can be produced in multiple interesting subregions through uploading the accurate phase pattern to the spatial light modulator (SLM) with the software. The focus array can be scanned with a two-mirror galvo scanner by scanning the single beam that is incident on the SLM. The two photon fluorescence signal is recorded directly with an electron-multiplying CCD in parallel. The two photon fluorescence images in the whole field-of-view are obtained under the different modes such as 10×10 and 50×50 arrays, and the multiple subregions of interest are addressably excited simultaneously. Compared with the other MMMs, our MMM has a good flexibility without sacrificing of the imaging speed and spatial resolution and also without hardware changes.