A microarray analysis method, in which a microarray obtained by arranging probes on a substrate surface having an irregular shape is irradiated with excitation light and fluorescence amounts of the probes excited by the excitation light are obtained as numerical data, includes a step (a) of measuring the fluorescence amounts of the probes to acquire fluorescence image data, a step (b) of receiving reflected light and/or scattered light from the substrate surface to acquire the irregular shape of the substrate surface of the microarray as alignment image data based on the light receiving intensities of the light, and a step (c) of determining positions of the probes on the fluorescence image data based on the alignment image data.