Abstract: In this study, the methods of fish environmental DNA (eDNA) capture, extraction and preservation were optimized by Droplet Digital PCR (ddPCR) quantitative technology using Carassius auratus in the laboratory, and the direct PCR technology without DNA extraction was preliminarily explored. The results showed that the mixed cellulose ester membrane produced the most ddPCR product, among the six kinds of filter membrane, and the polycarbonate membrane produced the lowest ddPCR product with only 1/17 of mixed cellulose ester membrane. The method which extracted the highest amount of DNA was the Qiagen DNeasy PowerWater kit, and the lowest was the high-salt method. The Qiagen DNeasy PowerWater kit yielded better results compared to the high-salt method, showing a 5.5-fold improvement in DNA yield. Different filter membranes and extraction methods have significant interactions on the total amount of final ddPCR product (P<0.001), filtration through the mixed cellulose ester membranes and Qiagen DNeasy PowerWater kit significantly outperformed other combinations of capture and extraction methods. Filter membranes stored at –20℃ or stored in Longmire's buffer solution recovered the most ddPCR product. The results of direct PCR amplification without DNA extraction showed that the high-fidelity enzyme of Vazyme can directly amplify the water samples and obtain the target DNA product. This study, compared the key steps in the eDNA operation process in detail, and the optimal protocol of fish eDNA sample processing and preservation was determined, which provided a reference for the establishment of eDNA standardized experimental process.