A biochip image analysis system comprises an image storage unit storing image information including an original image of the biochip including genes extracted from experimental and control groups' samples tagged by fluorescent dyes of different colors; an image converter converting the original image into a test image, generating an overlapped image and a color image; an edge detector separating spots of the test image into segments and detecting edges from spot and background areas to measure expression degrees of genes; a blob detector detecting blobs from the spot and background areas to generate a blob template; a blob remover generating a spot template and a background template; a data processor calculating statistical data and correcting intensity; and a data storage unit storing the data.