Amino acids, natural small molecules that are important materials for constituting living organisms, play important roles in natural products biosynthesis. Tryptophan has a unique indole ring structure which possesses more modification sites than other amino acids. In studies on microbial natural products biosynthesis, tryptophan and its derivatives often serve as structural moieties that are incorporated into the natural products structures. Here, we summarize different modification patterns of tryptophan, including alkylation, halogenation, hydroxylation, indole ring-open and rearrangement reactions. Analyzing and summarizing the enzymatic modifications of tryptophan could help us understand the structure diversities of natural products and lay the foundation for our study of the mechanism of the novel natural product biosynthesis.