This paper proposes a three-layer hierarchical voltage control strategy for distribution networks considering the customized charging navigation of electric vehicles (EVs). In the first layer, optimal power flow (OPF) is performed to determine the day-ahead dispatch of on-load tap changer (OLTC) and capacitor banks (CBs). The optimization problem is formulated as a mixed-integer second-order cone programming (MISOCP) which can be effectively solved. In the second layer, a customized charging navigation strategy is proposed to conduct the charging behaviors of EVs based on their own preferences. The novel preference modes are designed for different types of EV users to include not only the charge and time cost, but also the willingness to participate in voltage regulation service (VRS). The navigation problem is formulated as a mixed-integer linear programming (MILP), which is then solved by CPLEX solvers embedded with Dijkstra algorithm. In the third layer, charging stations measure local voltage and regulate the charging power of EVs to mitigate voltage violation. The charging selection and power allocation process are performed dynamically considering the mutual effect between the second and third layers. The economic compensation mechanism is also designed for both EV users and charging stations. The proposed approach is tested on the IEEE 33-bus distribution system coupled with a 24-bus transportation system, and simulation results verify the effectiveness both in charging navigation and mitigating voltage violation.