We report the electronic band structure and interlayer coupling induced phonon-glass–electron-crystal behavior in the van der Waals heterostructure PtSe2/γ-GeSe. The heterostructure is dynamically stable and possesses an indirect band gap of 0.63 eV (at the Heyd–Scuseria–Ernzerhof functional level) with type II band alignment. A low conduction band offset of 0.20 eV compared to the valence band offset of 0.92 eV suggests fluent electrons drive from γ-GeSe to PtSe2. Interlayer coupling induced strong phonon coupling and a unique “avoided crossing” feature between longitudinal acoustic and low-lying optical phonon modes between K and Γ points. Significant suppression of acoustic phonon modes and giant phonon scattering rates (a maximum value of 73.76 ps–1) results in a low lattice thermal conductivity of 1.20 W/(m·K) at 300 K after enforcing the mandatory rotational invariance condition. The calculated lattice thermal conductivity is 14-fold smaller than that of monolayer PtSe2 (16.97 W/(m·K)). The lattice thermal conductivity upsurges by 24% as the out-of-plane acoustic phonon dispersion undergoes linear dispersion, indicating the importance of pure quadratic flexural phonon dispersion. Our results disclose a strategy for having the phonon-glass–electron-crystal character in van der Waals heterostructures.