The invention discloses a method and system for improving uplink capacity of a remote radio unit (RRU) merged cell. The method comprises the following steps: multiple RRUs are connected to a baseband processing unit (BBU) of a base station, and the RRUs form a logic cell; the multiple RRUs report RTWP values of each sector at the same frequency point to the BBU unit through an Ir interface; the BBU reports the RTWP values of all sectors at the same frequency point under the logic cell to an RNC through a non-standard Iub interface; and the RNC receives the RTWP value of each sector at the same frequency point under the logic cell and a ground noise value of each sector under the logic cell, calculates the RoT of all sectors under the logic cell, and controls the uplink capacity of each sector according to the RoT of each sector and an RoT threshold. Thereby, the problem that part of the sectors have relatively large uplink capacity and other sectors cannot be accessed or have poor experience in case that the multiple RRUs are merged to the logic cell can be solved, and the uplink capacity of the multi-RRU merged cell can be improved.