Identification and control of topological phases in topological thin films offer great opportunities for fundamental research and the fabrication of topology-based devices. Here, combining molecular beam epitaxy, angle-resolved photoemission spectroscopy, and ab initio calculations, we investigate the electronic structure evolution in (Bi_1–xIn_x)₂Se₃ films (0 ≤ x ≤ 1) with thickness from 2 to 13 quintuple layers. By employing both thickness and In substitution as two independent “knobs” to control the gap change, we identify the evolution between several topological phases, i.e., dimensional crossover from a three-dimensional topological insulator to its two-dimensional counterpart with gapped surface state, and topological phase transition from a topological insulator to a normal semiconductor with increasing In concentration. Furthermore, by introducing In substitution, we experimentally demonstrated the trivial topological nature of Bi₂Se₃ thin films (below 6 quintuple layers) as two-dimensional gapped systems, consistent with our theoretical calculations. Our results provide not only a comprehensive phase diagram of (Bi_1–xIn_x)₂Se₃ and a route to control its phase evolution but also a practical way to experimentally determine the topological properties of a gapped compound by a topological phase transition and band gap engineering.