In this work, the waiting time distribution (WTD) statistics of electron transport through a two-channel quantum system in a strong Coulomb blockade regime and non-interacting dots are investigated by employing a particle-number resolved master equation with the Born–Markov approximation. The results show that the phase difference between the two channels, the asymmetry of the dot-state couplings to the left and right electrodes, and Coulomb repulsion have obvious effects on the WTD statistics of the system. In a certain parameter range, the system manifests the coherent oscillatory behavior of WTDs in the strong Coulomb blockade regime, and the phase difference between the two channels is clearly reflected in the oscillation phase of the WTDs. The two-channel quantum dot (QD) system for non-interacting dots manifests nonrenewal characteristics, and the electron waiting time of the system is negatively correlated. The different phase differences between the two channels can clearly enhance the negative correlation. These results deepen our understanding of the WTD statistical properties of electron transport through a mesoscopic QD system and help pave a new path toward constructing nanostructured QD electronic devices.