The invention discloses a method for self-configuring physical cell identifiers (PCI) for a honeycomb mobile communication network. The method comprises the following steps that: a network self-organization server collects the geographic position, antenna height, direction angle and downtilt information of a new base station; based on an experience path propagation model of the geographic position of the new base station, the network self-organization server calculates a path loss value and an antenna gain value between all base stations and determines a propagation loss value between all base stations; and by using a graph theory method, the network self-organization server globally optimizes reusing distances of the PCIs, allocates the optimized PCIs to the new base station, and then validates and screens the available PCIs by using a neighbor cell relationship list, so that interference between the base stations in which the same PCIs are used, and the PCIs can be accurately and reasonably configured. The method is applicable to automatic allocation of appropriate PCIs to the new base station which is not configured with the PCIs. By adoption of the method, configuration of the PCIs for the new base station can be quickly, conveniently and automatically finished, and the theoretical optimum performance can be realized.