With energy and environmental issues becoming increasingly prominent, electric vehicles (EVs) have become the important transportation means in the logistics distribution. In the real-world urban road network, there often exist multiple paths between any two locations (depot, customer, and charging station) since the time-dependent travel times. That is, the travel speed of an EV on each path may be different during different time periods, and thus, this paper explicitly considers path selection between two locations in the time-dependent electric vehicle routing problem with time windows, denoted as path flexibility. Therefore, the integrated decision-making should include not only the routing plan but also the path selection, and the interested problem of this paper is a time-dependent electric vehicle routing problem with time windows and path flexibility (TDEVRP-PF). In order to determine the optimal path between any two locations, an optimization model is established with the goal of minimizing the distance and the battery energy consumption associated with travel speed and cargo load. On the basis of the optimal path model, a 0-1 mixed-integer programming model is then formulated to minimize the total travel distance. Hereinafter, an improved version of the variable neighborhood search (VNS) algorithm is utilized to solve the proposed models, in which multithreading technique is adopted to improve the solution efficiency significantly. Ultimately, several numerical experiments are carried out to test the performance of VNS with a view to the conclusion that the improved VNS is effective in finding high-quality distribution schemes consisted of the distribution routes, traveling paths, and charging plans, which are of practical significance to select and arrange EVs for logistics enterprises.