A cell search system for a mobile station in a time division duplex system includes: a primary synchronization code search module for searching primary synchronization codes and comparing frame values of the primary synchronization codes to determine a position of the maximum value; a correlation module for estimating a phase value and acquiring a first correlation value; a secondary synchronization code search module for generating determinative variables and storing them based on the position of the maximum value; a comparison and decision module for detecting a maximum value of the determinative variables, comparing it with the values stored in the secondary synchronization code search module to count matching values, and comparing the count value with a system value to decide whether slot synchronization and group acquisition is successful; and a base station determination module for determining a second correlation value between midamble codes and the received signals, and selecting a maximum value of it to determine a base station.