Transition metal dichalcogenides layered nano‐crystals are emerging as promising candidates for next‐generation optoelectronic and quantum devices. In such systems, the interaction between excitonic states and atomic vibrations is crucial for many fundamental properties, such as carrier mobilities, quantum coherence loss, and heat dissipation. In particular, to fully exploit their valley‐selective excitations, one has to understand the many‐body exciton physics of zone‐edge states. So far, theoretical and experimental studies have mainly focused on the exciton–phonon dynamics in high‐energy direct excitons involving zone‐center phonons. Here, ultrafast electron diffraction and ab initio calculations are used to investigate the many‐body structural dynamics following nearly‐ resonant excitation of low‐energy indirect excitons in MoS2. By exploiting the large momentum carried by scattered electrons, the excitation of in‐plane K‐ and Q‐ phonon modes are identified with 𝑬′ symmetry as key for the stabilization of indirect excitons generated via near‐infrared light at 1.55 eV, and light is shed on the role of phonon anharmonicity and the ensuing structural evolution of the MoS2 crystal lattice. The results highlight the strong selectivity of phononic excitations directly associated with the specific indirect‐ exciton nature of the wavelength‐dependent electronic transitions triggered in the system.