Based on the modified Rytov variance, the effect of partially coherent beam through atmospheric turbulence on log-intensity variance is studied using the Gaussian-Schell model (GSM) beam and Andrews model. The log-intensity variance is deduced and discussed when partially coherent beam goes through weak turbulence and strong turbulence. The results show that the log-intensity variance of the partially coherent beam is lower than that of the fully coherent beam under the same turbulence conditions, as the light source coherence becomes worse, the log-intensity variance and the influence of turbulence plane decreases. The light source coherence, atmospheric refractive index structure constant and other parameters all have great effect on scintillation in both of weak and strong turbulence.