By using three atmospheric turbulence power spectrum models, namely Kolmogorov spectrum、 modified Hill spectrum and improved Rytov model, we obtain the relationship between scintillation index and atmospheric refractive index structure constant on detection path of residual turbulent scintillation lidar. Changes of turbulence intensity under difference inner scales are analyzed and compared with the situation that not considering the inner scale. The influence of inner scale on the detection of turbulence by residual turbulent scintillation lidar is analyzed according to experimental data. The results show that, in the range of inner scale, by using the modified Hill spectrum, the ratio of refractive index structure constant of the infinite inner scale to refractive index structure constant of not considering the inner scale is 9 in theory, and deviations are 0.4/0.1 orders in experiment at propagation distance of 1020 m and 2040 m, respectively. When we use the improved Rytov model, the ratio of refractive index structure constant of the infinite inner scale to refractive index structure constant of not considering the inner scale is 6, and deviations are 0.6/0.3 orders in experiment at propagation distance of 1024 m and 2040 m, respectively. Theoretical and experimental results show that, to some extent, the refractive index structure constant of the infinite inner scale is deviated from the situation of not considering the inner scale, which is related to propagation distance and the magnitude of inner scale. Therefore, inner scale must be considered in the detection of residual turbulent scintillation lidar.