Two-dimensional metal chalcogenides (2D-MCs) with complex interactions are usually rich in phase transition behavior, such as superconductivity, charge density wave (CDW), and magnetic transitions, which hold great promise for the exploration of exciting physical properties and functional applications. Interlayer chemical modulation, as a renewed surface modification method, presents congenital advantages to regulate the phase transitions of 2D-MCs due to its confined space, strong guest-host interactions, and local and reversible modulation without destructing the host lattice, whereby new phenomena and functionalities can be produced. Herein, recent achievements in the interlayer chemical modulation of 2D-MCs are reviewed from the aspects of superconducting transition, CDW transition, semiconductor-to-metal transition, magnetic phase transition, and lattice transition. We systematically discuss the roles of charge transfer, spin coupling, and lattice strain on the modulation of phase transitions in the guest-host architectures of 2D-MCs established by electrochemical intercalation, solution-processed intercalation, and solid-state intercalation. New physical phenomena, new insight into the mechanism of phase transitions, and derived functional applications are presented. Finally, a prospectus of the challenges and opportunities of interlayer chemical modulation for future research is pointed out.