This study investigated the extraction method of Auricularia auricula-judae melanin, focusing on the tough cell wall of the fruiting body and its free radical scavenging ability and antioxidant effects on Caenorhabditis elegans. The biological enzymatic method was performed to break the cell wall and prepare melanin extract. Further, extraction conditions were optimized using the Box-Behnken design. The in vitro free radical scavenging ability of melanin and its antioxidant effects on C. elegans were also studied. The results showed that A. auricula-judae melanin had strong absorption at a wavelength of 192 nm, with a absorbance-concentration equation of y = 0.7042x + 0.2114. Enzyme extraction under the following conditions yielded melanin of 2.21% ± 0.03%: 150 min, enzyme-to-substrate ratio of 1.1%, pH 4.4, 50°C, and 52 min. Free radical scavenging ability of A. auricula-judae melanin to superoxide anion-, ABTS+., and OH· radicals was concentration dependent. For example, at a concentration of 1 mg/mL, the scavenging rate of these free radicals was 85.71% ± 0.02%, 91.34% ± 0.01%, and 91.81% ± 0.01%, respectively. A. auricula-judae melanin could significantly prolong the lifespan of C. elegans (P < 0.05), and enhance locomotion behavior of C. elegans compared with the worms in the vehicle group (P < 0.05).