Environmental DNA (eDNA) analysis is a powerful tool within ecology for the distribution or abundance study of aquatic species. DNA extracting was an indispensable process to employ this method. In eDNA extracting of macro-organisms, DNeasy Blood and Tissue Kit was commonly used, but its price was about 80 RMB/sample, which was too expensive. Cheaper eDNA extraction kit was a potential aspect for improvement to expand further application of eDNA analysis. In order to examine some cheaper kits’ effectiveness of extracting eDNA of macro-organisms and select an optional low-cost kit, a test among three kits was held. 12S rRNA bands of marine fishes on the agarose gel preliminarily revealed that all three kits could successfully extract eDNA from field water samples. Digital PCR results further revealed that the average eDNA concentration of Sepiella japonica extracted by three kits were (4.62 ± 0.72) × 105, (3.83 ± 0.56) × 105, and (2.35 ± 0.27) × 105 copies/300 ml, respectively. The eDNA concentrations by AxyPrep DNA Gel Extraction Kit were about 83% of that extracted by DNeasy Blood and Tissue Kit. However, extracting cost of an eDNA sample using AxyPrep DNA Gel Extraction Kit was about 3.75% of that using DNeasy Blood and Tissue Kit. Up to now, many eDNA surveys have collected eDNA samples with large scale, which sometimes required hundreds of filter membranes and a mass of extraction kits. Combined the price and effectiveness, using AxyPrep DNA Gel Extraction Kit as an substitute for DNeasy Blood and Tissue Kit could remarkably cut the eDNA extracting cost. AxyPrep DNA Gel Extraction Kit might be an optional low-cost method of extracting environmental DNA of macro-organisms from filter membranes in large scale eDNA surveys.