A microscopy imaging system is disclosed. The system includes: a femtosecond laser; an acousto-optic modulator, configured to periodically modulate an intensity of a laser light; a line-scanning component, configured to focus the laser light to form a line-shaped beam and to scan in a direction perpendicular to the line-shaped beam; a chromatic dispersion component, configured to generate spatial chirped laser pulses; a collimating lens, configured to converge components with different wavelengths dispersed by the chromatic dispersion component to propagate in parallel; a microscope component, configured to guide light passing through the collimating lens to illuminate the sample and capture a fluorescence image at a focal plane; and a synchronous control component, configured to synchronously control the acousto-optic modulator to modulate the intensity of the laser light, the line-scanning component to scan and the microscope component to capture fluorescence images, such that a reconstructed image is obtained according to the images.