[Purposes] Aiming at commuting concentration and traffic congestion caused by a single work hour in the urban morning peak, this paper built a multi-mode travel equilibrium model with dual work hours to reveal the mechanism of work hour heterogeneity and time interval on commuting equilibrium. This can theoretically support the formulation of staggered work hour policy. [Methods] A private car-subway system was chosen as the research object, and combined with bottleneck congestion model and subway congestion calculation method. In addition, the equilibrium equations under time-cost-quantity constraints were constructed considering commuters′ work hour preference heterogeneity. The characteristics of equilibrium modes were analyzed and the AMPL-Minos optimizer was applied for solutions and verification. [Findings] Compared with single work hour travel, heterogeneous work hour travel reduces the social travel cost by 15% on average, with the optimal effect of 25% reduction under a 50∶50 proportion of travelers and 2.0 h time interval. Expanding the freedom of work hour selection can further reduce social travel cost. [Conclusions] Work hour interval affects travel costs by regulating the threshold of equilibrium mode, causing them to exhibit a phased characteristic of “decline-stability”. For the same travel mode, the proportion of travelers is positively correlated with the equilibrium cost. Work hour heterogeneity and multi-mode coordinated equilibrium are effective ways to alleviate morning peak congestion.