Based on the data from fishery resource acoustic surveys in central South China Sea from February to March 2012, using Virtual Variable Module of Echoview system, the effects of subtracting background noise on echogram, Ping echogram, Nautical Area Scattering Coefficient (NASC) and Volume Backscattering Strength (Sv) were investigated. The results showed that the interference of background noise on 120 kHz transducer was much stronger than that on 38 kHz transducer. After subtracting background noise, the variation of echogram from 120 kHz transducer was much more obvious than that from 38 kHz as the depth range increases; as the Sv at 1 m to the transducer surface (Sv1m for short) changed,the variation of NASC and Sv differentiated obviously between frequencies in the same depth-layer and the extent of variation was dependent on the depth layers,and the variation of NASC and Sv from transducer of the same frequency differentiated obviously between depth layers too. The distinguishing features of variation of NASC and Sv were important bases for determining Sv1m. According to the analysis, it was absolutely essential to remove background noise in the post-processing of fishery acoustic data; background noise could be removed well by this method, which was a valid means of enhancing the accuracy of acoustic estimation.