A centralized base station system based on ATCA, comprising a main base station subsystem and one or more remote radio frequency subsystems, the main base station subsystem comprising: one or more shelves based on ATCA platform, each shelf comprising at least one control switch module of ATCA board form; one or more base station controller interface module; a signaling module; one or more baseband processing modules; one or more remote radio frequency interface modules; a first switch network comprising first switch network shelf back board BASE interface link, a control switch module and a first network switch unit; a second switch network comprising a shelf back board FABRIC interface link, a control switch module and a second network switch unit; a clock synchronization network comprising a shelf back board clock synchronization bus, a control switch module and a clock unit; and a signal transmission network, wherein the second network switch unit and the clock unit are further connected to the first network switch unit, one of the control switch modules of all the shelves is the main control module.