By analyzing the influence of stochastic perturbation matters on vehicle path optimization, a perturbation scheduling model for logistics and distribution with a carbon tax mechanism is established under the premise of time window variation and load capacity constraints. Herein, we propose an enhanced Genetic Algorithm (GA) based on a Gaussian matrix mutation (GMM) operator, which maintains the diversity of the population while speeding up the algorithm’s convergence. The model builds a Gaussian probability matrix using the site positional order distribution characteristics implied in the original site data information, and applies the Gaussian probability matrix to individual gene mutations using a roulette-wheel-selection method; thus, the study guarantees the genetic diversity of the population while guiding it to evolve in the high-fitness direction. Finally, an experimental simulation is performed using data obtained from a commercial supermarket, thereby verifying the effectiveness of the proposed algorithm and comparing it with other algorithms. The results reveal that compared with the classical GA, the average convergence speed of the improved GA can be increased by 50–60% and the consumed algorithm time can be reduced by 48% while maintaining the difference in solution accuracy within 1%.