A star sensor fast tracking window image processing system, comprising: a CPU and an FPGA; wherein the CPU is configured to generate tracking window control data of a navigation star selected according to navigation star positions in a star library for the star sensor and for calculating a star centroid of the navigation star, the FPGA comprises: a tracking window control memory, a tracking window collecting module configured to read tracking window control data, a tracking window data memory for collecting pixel clusters according to the tracking window control data, and storing grey values of all pixels in the pixel clusters, a pixel cluster first pixel address memory, and a pixel cluster processing module; wherein tracking windows are constituted by dividing a detector image plane of the star sensor according to ZxZ pixels, wherein, Z is a positive integer; the tracking window control data is control information for a collected tracking window, the ZxZ pixels forming a pixel cluster of the collected tracking window; the CPU is configured to write the tracking window control data into the tracking window control memory, and write a first pixel address of a pixel cluster for pixel clusters of collected tracking windows into the pixel cluster first pixel address memory; the tracking window collecting module is configured to read the tracking window control data in the tracking window control memory, and collect pixel clusters according to the tracking window control data; the pixel cluster processing module is configured to read the first pixel address of the pixel cluster in the pixel cluster first pixel address memory and extract pixel clusters centered on the navigation star position according to the first pixel address of the pixel cluster, traverse all the pixels of the pixel cluster centered on the navigation star position, calculate a mean grey value of all the pixels as an estimated background, then traverse all the pixels of the pixel cluster centered on the navigation star position based on the estimated background, and extract a characteristic vector of a star centroid of the navigation star; and the CPU is further configured to read the characteristic vector of the star centroid and calculate the star centroid according to the characteristic vector. tracking windows are constituted by dividing a detector image plane of the star sensor according to ZxZ pixels, wherein, Z is a positive integer; the tracking window control data is control information for a collected tracking window, the ZxZ pixels forming a pixel cluster of the collected tracking window; the CPU is configured to write the tracking window control data into the tracking window control memory, and write a first pixel address of a pixel cluster for pixel clusters of collected tracking windows into the pixel cluster first pixel address memory; the tracking window collecting module is configured to read the tracking window control data in the tracking window control memory, and collect pixel clusters according to the tracking window control data; the pixel cluster processing module is configured to read the first pixel address of the pixel cluster in the pixel cluster first pixel address memory and extract pixel clusters centered on the navigation star position according to the first pixel address of the pixel cluster, traverse all the pixels of the pixel cluster centered on the navigation star position, calculate a mean grey value of all the pixels as an estimated background, then traverse all the pixels of the pixel cluster centered on the navigation star position based on the estimated background, and extract a characteristic vector of a star centroid of the navigation star; and the CPU is further configured to read the characteristic vector of the star centroid and calculate the star centroid according to the characteristic vector.