As to the high Peak to Average Power Ratio (PAPR) issue in OFDM system, the paper has proposed a clipping algorithm based on the Particle Swarm Optimization (PSO).The algorithm takes advantage of the splendid searching ability of the PSO to calculate the best threshold and takes advantages of strong controlling ability and easy implementation of the clipping to clip the signal sequences. It takes the steps of iterative searching, clipping, filtering etc. to search the best particle, i.e. the excellent threshold to obtain the lowest PAPR with the precondition of the set CCDF, achieving the target of reducing the system PAPR. It presents comparisons of BER and CCDF between the linearly decreasing weight (LDW) and fixed inertia weight. The simulations show that, compared with the simple clipping algorithm, by using the proposed algorithm no extra BER is brought but the target of reducing PAPR in the low SNR area is achieved, so the proposed algorithm is of vital significance to improving the performance of the whole system.