This paper developed a mixed multinomial probit (MMNP) model with alternative error specification and random coefficients (for both generic variables and personal attributes) to accommodate flexible covariance structure and taste variation. The MMNP model can be efficiently estimated with analytic approximations of multivariate normal cumulative distribution functions, which avoid defects of simulation-based integration in the mixed multinomial logit (MMNL) model. The integral dimension of the MMNL model increases as random coefficients increase, but it only depends on the number of available alternatives in the MMNP model. Simulation experiments and empirical analysis of Shanghai commuters’ mode choice behavior were undertaken to examine the performance of MMNP models. Both simulation results and empirical results show that MMNP models can well accommodate flexible covariance structures and taste variation reflected through random coefficients being associated with both generic and personal variables. Empirical results indicate that the MMNP model performs better than traditional discrete choice models, such as the multinomial logit, the cross-nested logit, MMNL, and multinomial probit models. Random coefficients of “in-vehicle time of car” and “number of companions” indicate taste heterogeneity and the identifiability of random coefficients associated with both generic and personal attributes. Pairwise positive correlations between car/taxi, bus/metro, and bus/bus and metro are to be expected. However, the positive correlation between the car and metro modes may be unique to the Chinese city, Shanghai, because of the developed metro system. Unequal error variances reflect heterogeneities in unspecified factors in commute modes’ utilities. The MMNP model will offer an alternative efficient way to accommodate taste heterogeneity and flexible error covariance structure in discrete choice models. Compared with the MMNL model, the MMNP model can accommodate more random coefficients without increasing computational complexity.