By handling the travel cost function artfully, the authors formulate the transportation mixed network design problem (MNDP) as a mixed-integer, nonlinear bilevel programming problem, in which the lower-level problem, comparing with that of conventional bilevel DNDP models, is not a side constrained user equilibrium assignment problem, but a standard user equilibrium assignment problem. Then, the bilevel programming model for MNDP is reformulated as a continuous version of bilevel programming problem by the continuation method. By virtue of the optimal-value function, the lower-level assignment problem can be expressed as a nonlinear equality constraint. Therefore, the bilevel programming model for MNDP can be transformed into an equivalent single-level optimization problem. By exploring the inherent nature of the MNDP, the optimal-value function for the lower-level equilibrium assignment problem is proved to be continuously differentiable and its functional value and gradient can be obtained efficiently. Thus, a continuously differentiable but still nonconvex optimization formulation of the MNDP is created, and then a locally convergent algorithm is proposed by applying penalty function method. The inner loop of solving the subproblem is mainly to implement an all-or-nothing assignment. Finally, a small-scale transportation network and a large-scale network are presented to verify the proposed model and algorithm.