Interference approximation method (IAM), one of the channel estimation methods for orthogonal frequency division multiplexing/offset quadrature amplitude modulation (OFDM/OQAM) system, is a usual method which has a high estimation accuracy. However, in processing of transmission and receiving of the OFDM/OQAM signal, the signal can be influenced by clipping of high power amplifier (HPA) which can lead to a recession of the IAM channel estimation accuracy. To research the influences of different IAM structures, aiming at peaktoaverage ratio of pilot, this article proposes a partcomplementary cumulative distribution function, researches the bit error ratio performance of the system and normalizes mean square error performance of channel estimation in different clipping thresholds of IAM channel estimation accuracy. To compensate the influence of the HPA clipping effect, this article proposes a method of clipping compensation. This method does not need to transmit extra clipping information and just calculates with the pilot structure and compensates at the receiver. Simulation result shows that the method works and the worse the clipping influence, the better the compensation effect.