The invention discloses an air interface synchronization method, a base station, and a system. The method includes: a first base station generates a first synchronization reference signal, wherein the first base station is one of M base stations in the Nth small cell, the first synchronization reference signal and the first base station are positioned in the Nth small cell, synchronization reference signals of other base stations except for the first base station are orthogonal to each other, N is a positive integer greater than or equal to 2, M is a positive integer greater than or equal to 1, and the first base station sends the first synchronization reference signal at a preset synchronous subframe.