Abstract We demonstrated an ultrafast time-resolved measurement method operating at the single-photon level and employing a two-color comb-based asynchronous optical sampling (ASOPS) setup. We harnessed the two-color ASOPS photon counting approach to achieve long-term averaging of the ultralow intensity signal with a synchronized optical trigger signal, which minimizes residual timing jitter between the two combs. A pulse-width limited picosecond cross-correlation signal was successfully obtained with a power level of <1 photon/pulse. This approach enables the thorough study of ultrafast time-resolved detection of entangled photon pairs, quantum mechanical correlations in the time-frequency domain and finds wide use in optical quantum technology.