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This paper investigates the morning commuter problem in a competitive highway/transit network with stochastic capacity which follows uniform distribution. It is assumed that both the commuters’ departure time choice and modes choice follow the user equilibrium (UE) principle in terms of the mean travel cost. Taking account of the effect of the stochastic capacity, the analytical solution of the proposed stochastic bottleneck model is derived. The toll differentiation has been analyzed as efficient measures to address growing traffic congestion problems in bi-modal travel system. Both analytical and numerical results show that the stochastic capacity indeed changes the commuters’ travel choice pattern during the rush hour. The sensitivity analyses combined the degraded capacity with other elements are also investigated.