With the widespread application of quantum communication technology, there is an urgent need to enhance unconditionally secure key rates and capacity. Measurement-device-independent quantum key distribution (MDI-QKD), proven to be immune to detection-side channel attacks, is a secure and reliable quantum communication scheme. The core of this scheme is Hong–Ou–Mandle (HOM) interference, a quantum optical phenomenon with no classical analog, where identical photons meeting on a symmetric beam splitter (BS) undergo interference and bunching. Any differences in the degrees of freedom (frequency, arrival time, spectrum, polarization, and the average number of photons per pulse) between the photons will deteriorate the interference visibility. Here, we demonstrate 16-channel weak coherent pulses (WCPs) of HOM interference with all channels’ interference visibility over 46% based on two independent frequency-post-aligned soliton microcombs (SMCs). In our experiment, full locking and frequency alignment of the comb teeth between the two SMCs were achieved through pump frequency stabilization, SMC repetition rate locking, and fine tuning of the repetition rate. This demonstrates the feasibility of using independently generated SMCs as multi-wavelength sources for quantum communication. Meanwhile, SMC can achieve hundreds of frequency-stable comb teeth by locking only two parameters, which further reduces the complexity of frequency locking and the need for finding sufficient suitable frequency references compared to independent laser arrays.