Measurement-device-independent quantum key distribution (MDI-QKD) protects legitimate users from attacks on measurement devices. The decoy method allows for unconditionally secure quantum key generation using lasers. One of the most important issues in MDI-QKD is that photons from two independent lasers must be indistinguishable. Because Alice and Bob send Charlie laser pulses through separate fiber links, the arrival times of the pulses fluctuate independently. According to the Hong-Ou-Mandel (HOM) interference at Charlie's relay, the time delay between two photons has the greatest effect on distinguishability. However, to date, these effects have not been analyzed. Our study uses simulations to investigate the effects of two-photon temporal distinguishability in terms of the visibility of the HOM-dip of two photons on the final key rate of finite-size MDI-QKD. Furthermore, an acceptable time delay range was estimated based on photons with Gaussian spectral amplitude functions.INDEX TERMS Measurement-device-independent quantum key distribution, decoy method, Hong-Ou-Mandel interference, time delay This article has been accepted for publication in IEEE Transactions on Quantum Engineering.