Arylalkylamine N‐acetyltransferase (AANAT) serves as a key enzyme in the biosynthesis of melatonin by transforming 5‐hydroxytryptamine (5‐HT) to N‐acetyl‐5‐hydroxytryptamine (NAS), while its low activity may hinder melatonin yield. In this study, a novel AANAT derived from Sus scrofa (SsAANAT) was identified through data mining using 5‐HT as a model substrate, and a rational design of SsAANAT was conducted in the quest to improving its activity. After four rounds of mutagenesis procedures, a triple combinatorial dominant mutant M3 was successfully obtained. Compared to the parent enzyme, the conversion of the whole‐cell reaction bearing the best variant M3 exhibted an increase from 50% to 99% in the transformation of 5‐HT into NAS. Additionally, its catalytic efficiency (kcat/Km) was enhanced by 2‐fold while retaining the thermostability (Tm > 45 °C). In the up‐scaled reaction with a substrate loading of 50 mM, the whole‐cell system incorporating variant M3 achieved a 99% conversion of 5‐HT in 30 h with an 80% yield. Molecular dynamics simulations were ultilized to shed light on the origin of improved activity. This study broadens the repertoire of AANAT for the efficient biosynthesis of melatonin.