Shack-Hartmann wavefront sensor is used to explore irradiance scintillation effect of light propagation through atmospheric turbulence, whose subaperture and corresponding CCD element are regarded as intensity detector system. Its principle is analyzed. Experiments on phase fluctuation and scintillation are preliminarily carried out in atmospheric boundary layer over 1000 m horizontal path. Compared with the measurement results of traditional large-aperture scintillometer, it is found that the method of Shack-Hartmann wavefront sensor is reliable with correlation coefficient of 0.838. At the same time, the daily variation trend of the refractive index structure constants retrieved from the two atmospheric turbulence effects is compared. The correlation coefficient of the two C2n reaches 0.798 in the log-log grid. All the experimental results indicate that simultaneous measurement of phase fluctuation and scintillation by Shack-Hartmann wavefront sensor is feasible, which extends the function of this sensor.