As a narrow-gap semiconductor, III-VI two-dimensional (2D) van der Waals layered indium selenide (InSe) has attracted a lot of attention due to excellent physical properties. For potential optoelectronic applications, the tunability of the optical property is challenging, e.g., the modulation of optical bandgap commonly by element doping. However, the deep understanding of the influence of element doping on the microstructure and the optical properties lacks of systematic investigation. In this work, by using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy, we investigate the influence of Bi doping on controlling of the microstructure and optical properties of InSe single crystal in detail. The results show that Bi doping can introduce additional stacking faults in InSe single crystal, and more importantly, the atomic spacing and lattice constant of Bi-doped InSe are changed a lot as compared to that of the undoped one. Further optical characterizations including photoluminescence and transmission spectra reveal that Bi-doping can broaden the transmission wavelength range of InSe and make its optical bandgap blue-shift, which can also be physically interpreted from the doping-induced structure change. Our work expands new ideas for the optical property modulation of 2D thin-layer materials and brings new possibilities for the development of thin-layer InSe optical devices.