The guarantee of the fast dynamics stability is essential for successful application of singular Perturbation technique to control systems design. Even though the fast dynamics of the control systems is rendered stable by an analog controller, the fast dynamics stability of the control systems resulted from an digital implementation of the analog controller can be impaired severely. In this paper, we first investigate the time sampling effects on singular perturbation based control systems by centering on a design example of recently developed singular perturbation based STT missile autopilot with high performance. The investigation shows that the stability margin the fast dynamics of the STT misile autopilot system decreases rapidly as the sampling interval of discretizing the analog autopilot increases. Under this analysis, we propose a composite digital controller with compensation for the decreasing stability margin of the fast dynamics due to time sampling to achieve better performance with respect to sampling time. The improved performance of the proposed composite digital controller is verified by simulation. This result shows that one needs to investigate time sampling effects in the digital implementation of singular perturbation based controllder, and then can have benefit from the investigation.