Quantum key distribution (QKD) system based on the basic principles of quantum mechanics can reach the level of information theory security. Single photon detector is an important component of QKD system, and the afterpulse probability has an important effect on the performance of QKD system. In this paper, an InGaAs/InP high sinusoidal gated detector afterpulse suppression scheme is designed to meet the requirements of QKD system.In this paper, according to the law that the probability of the afterpulse of the InGaAs/InP high-speed sinusoidal gated detector shows an exponential decreasing distribution with time, the detection pulse is measured by using the "Start-Stop" time interval measurement method. Each detection pulse is time-marked separately, and the probability of the afterpulse of the detector is reduced by discarding the detection pulse within a certain period of time (Fig.2).This paper actually verifies the relationship between the afterpulse probability and the discard time of a single photon detector (Fig.5). The main afterpulse distribution area is pointed out and the reason for the depression in the range of discard time is explained (Fig.6). The afterpulse probability under different discard time conditions was calculated.The afterpulse probability is 2.46% when the discard time is 500 ns, and 1.97% when the discard time is 5 μs. Furthermore, it is pointed out that distinguishing the arrival time of detection pulse by time measurement can also improve the ability of QKD system to resist quantum hacker attacks such as avalanche transition region attack and behind door attack.According to the law that the afterpulse probability of the InGaAs/InP high-speed sinusoidal gated detector is exponentially decreasing with time, a afterpulse suppression scheme based on time measurement is proposed in this paper. The afterpulse probability of the detector is reduced by marking the detection event with time and discarding the detection pulse in a period of time. The proposed afterpulse probability suppression scheme has the characteristics of clear principle and easy engineering implementation, and has no direct influence on the working process of single photon detector, but the detector saturation count rate will decrease with the increase of discard time. At the same time, distinguishing the arrival time of detection pulse by time measurement can also improve the ability of QKD system to resist quantum hacker attacks, and can support the application of high-speed sinusoidal gated single photon detector in QKD system.