Grain boundaries in two-dimensional (2D) semiconductors generally induce distorted band alignment and interfacial charge, which impair their electronic properties for device applications. Here, we report the improvement of band alignment at the grain boundaries of PtSe₂, a 2D semiconductor, with selective adsorption of a presentative organic acceptor, tetracyanoquinodimethane (TCNQ). TCNQ molecules show selective adsorption at the PtSe₂ grain boundary with strong interfacial charge. The adsorption of TCNQ distinctly improves the band alignment at the PtSe₂ grain boundaries. With the charge transfer between the grain boundary and TCNQ, the local charge is inhibited, and the band bending at the grain boundary is suppressed, as revealed by the scanning tunneling microscopy and spectroscopy (STM/S) results. Our finding provides an effective method for the advancement of the band alignment at the grain boundary by functional molecules, improving the electronic properties of 2D semiconductors for their future applications.