Abstract: It is meaningful to integrate the atmospheric scintillation measurement on the far field speckles projection imaging system for comprehensively analyzing the characteristics of laser atmospheric propagation and its influence on the photoelectric system. However, the atmospheric scintillation will become very weak at large receiving aperture because of aperture averaging effect, and the intensity fluctuation induced by laser source stability will become obvious. Therefore, an atmospheric scintillation measurement model considering the laser source intensity fluctuation is established based on the multiply stochastic process assumption of laser source intensity fluctuation and atmospheric scintillation. Using the characteristic that the laser source intensity fluctuation does not vary with aperture and the atmospheric scintillation varies with aperture, the atmospheric scintillation and laser source intensity fluctuation can be estimated respectively through the measurement model by combining the aperture averaging factor in weak fluctuation and the intensity scintillation measurement result with different receiving aperture at the same time in the projector optics. The experiment results show that the relative error between theoretical prediction and experimental values is below 9.685% at the aperture from 0.05 m to 0.40 m. This method could estimate the atmospheric scintillation in weak turbulence fluctuation based on the projection optics system.