A apparatus and method for allocating synchronization acquisition sequence in a time domain and allocating a cell ID search sequence in a frequency domain. In a method for transmitting a synchronization signal of a base station in a wireless communication system, a binary frequency-domain preamble sequence predetermined for cell ID search and a binary time-domain preamble sequence predetermined for synchronization acquisition are used to determine a complex time-domain preamble sequence except the binary time-domain preamble sequence among the time-domain preamble sequences that are generated according to an Inverse Fast Fourier Transform (IFFT) operation on the binary frequency-domain preamble sequence. The complex time-domain preamble sequence and the binary time-domain preamble sequence are transmitted to a mobile station.