A large scale cell image analysis method and system are provided. The method includes: obtaining a cell image; performing a region segmentation process; and performing a feature calculation process. The region segmentation process includes: performing a statistical intensity algorithm according to the cell image to calculate a first threshold and a second threshold; dividing the cell image into a background region and a cell region according to the first threshold; performing an average intensity process according to the cell region to calculate a third threshold and a fourth threshold; and dividing the cell region into a cytoplasmic region and a nucleus region according to the third threshold and the fourth threshold. The feature calculation process calculates at least one feature at least according to the cell region, the nucleus region, and the cytoplasmic region.