The qualitative and quantitative capability of the ion trap mass analyzer could be greatly affected by the accumulation time. However, the importance of the accumulation time has not so far been thoroughly explored. Here, the influence of ion accumulation time on qualitative and quantitative analysis of complicated components was systematically investigated based on the case study of 40 ophiopogonins in Ophiopogon extract by hybrid ion trap time-of-flight mass spectrometry (LCMS-IT-TOF). In this process, the accumulation time was set at 10, 25, 50, 100, and 200 ms, respectively. The effect of accumulation time on qualitative analysis of ophiopogonins was studied by comparing the total ion current (TIC) of MS1, TIC of MS2, and the number and signal of fragmental ions. The results demonstrated that the signal could be greatly influenced by varying the accumulation time. The number and signal of the fragmental ions were increased significantly with a longer accumulation time in the range of 10–100 ms. Also, the effect of accumulation time on quantitative analysis of ophiopogonins was investigated by comparing the linearity, accuracy, and precision measured on LCMS-IT-TOF. Importantly, quantitative parameters could all be significantly improved by choosing an appropriate accumulation time.