The invention provides an optimization method of an X-ray combined refractor focusing optical system. The optimization method uses an X-ray combined refractor series having different unit numbers and face type structures, an incident X-ray photon wavelength and an expected focal length as input design parameters, a selection and arrangement result of the X-ray combined refractors as an output design parameter, and the focal length of the focusing optical system as a first optimization condition, and obtains a primary optimization scheme according to the tolerance of the focusing optical system. The optimization method of the X-ray combined refractor focusing optical system provided by the invention optimizes parameters, improves performance, and expands the range of application.