In order to improve the repeatability of HPLC determination of cypermethrin in fungal degradation system, a pre-treatment method for HPLC analysis of cypermethrin in Aspergillus oryzaedegradation system was studied. A suitable pre-treatment method including sampling and extraction of cypermethrin from the A. oryzae degradation system was established. Total sampling could solve the uneven dispersion or distribution of cypermethrin in the degradation system. Acetonitrile extraction assisted with ultrasonic could make cypermethrin in or on the fungal cells be released more sufficiently. The determination of cypermethrin in the pretreated sample by HPLC showed a high precision (RSD=1.14%,n=5) and a good repeatability (RSD=1.70%~2.12%,n=5) as well as a good stability (RSD=1.57%,n=5). This method can provide an important reference for HPLC determination of pyrethroid in microbial degradation systems.