An alignment method based on pixel color and an alignment system for using the same is disclosed. The method includes: Step S1: retrieving a photoresistance eigenvalue of each subcolor resist illuminated by a light source and setting a pixel threshold according to the photoresistance eigenvalue; Step S2: performing a binarization process on a pixel according to the pixel threshold to obtain a binary pixel; and Step S3: calculating an alignment position according to the binary pixel and aligning the color resist according to the alignment position. The present invention avoids the distribution of metal traces and patterns of a color filter on array (COA) product, improves the stability of measuring the COA product, aligns pixel with different shapes, and edits the computing logic for measured positions. When the shape of the pixel is irregular, the reasonable logic is selected to define the measured positions.