The noise of fine tracking detectors in acquisition, tracking and pointing systems is different, which has different influences on the position location of light spots. The source of the strip noise of detectors is analyzed, and the influence of the strip noise on centroid algorithm is deduced theoretically. The threshold centroid algorithm is used to locate the light spots of images with stripe noise and salt and pepper noise, and location deviations of X axis and Y axis corresponding to different signal-to-noise ratios and different threshold values are simulated, and the light spot location accuracies of X axis and Y axis are compared. The simulation results show that the light spot location accuracy of X axis is better than that of Y axis when the stripe noise exists in Y axis direction. The tracking accuracies of X axis and Y axis of the fine tracking system under different system configurations and different interference amplitudes are experimentally tested. It proves that, for fine tracking system with two symmetrical orthogonal axes, the tracking accuracy of X axis is better than that of Y axis, which verifies that the location accuracy of X axis is better than that of Y axis when the stripe noise exists. The results obtained from simulation and experiment are identical.