Abstract: The timing relationship between base stations is asynchronous in W-CDMA sys-tem. So the three-step cell search algorithm is introduced in 3GPP protocols in order to identify the special base station quickly. The second step, Secondary Synchronous CHannel(S-SCH) ac-quisition, is much critical, but the computing complexity of the conventional matched filter bank method is very large. This paper proposes Partial Fast Hadamard Transform (PFHT) ac-cording to the S-SCH structural property, which extremely reduces the computing complexity to almost 70%. On the other hand, a distributed sub-graph search algorithm is put forward to save more complication than RS code table brute-force search. In a word, the hardware complexity is dramatically cut down by the improved scheme, which is valuable for engineering applications.