Abstract: An AI-assisted automatic labeling system and a method thereof are disclosed. The method comprises steps: selecting images from microscopic images as candidate images, using a pre-labeling module to automatically label cells in the candidate images, and dividing the labeled images into training data and verification data; using a training module and the training data to train a basic model; using a verification module to verify and modify the basic model, wherein the verification module respectively verifies at least one cell area and at least one background area of the verification data to converge the basic model and form an automatic labeling model; using the automatic labeling model to automatically label cells in redundant images of the microscopic images. The basic model trained by the present invention can use few labeled images to perform regressive training and verification and then automatically labels the redundant images accurately and efficiently.