This study proposes an improved truncated Newton (ITN) method for the logit-based stochastic user equilibrium problem. The ITN method incorporates a preprocessing procedure to the traditional truncated Newton method so that a good initial point is generated, on the basis of which a useful principle is developed for the choice of the basic variables. We discuss the rationale of both improvements from a theoretical point of view and demonstrate that they can enhance the computational efficiency in the early and late iteration stages, respectively, when solving the logit-based stochastic user equilibrium problem. The ITN method is compared with other related methods in the literature. Numerical results show that the ITN method performs favorably over these methods.