Abstract SPT0311-58 is the most massive infrared luminous system discovered so far during the Epoch of Reionization (EoR). In this paper, we present a detailed analysis of the molecular interstellar medium at z = 6.9, through high resolution observations of the CO(6–5), CO(7–6), CO(10–9), C i (2–1), and p‐H 2 O(2 1,1 −2 0,2 ) lines and dust continuum emissions with the Atacama Large Millimeter/submillimeter Array. The system consists of a pair of intensely star-forming, gravitationally lensed galaxies (labeled West and East). The intrinsic far-infrared luminosity is (16 ± 4) × 10 12 L ⊙ in West and (27 ± 4) × 10 11 L ⊙ in East. We model the dust, CO, and C i using non-local thermodynamic equilibrium radiative transfer models and estimate the intrinsic gas mass to be (5.4 ± 3.4) × 10 11 M ⊙ in West and (3.1 ± 2.7) × 10 10 M ⊙ in East. We find that the CO spectral line energy distribution in West and East are typical of high-redshift submillimeter galaxies (SMGs). The CO-to-H 2 conversion factor ( α CO ) and the gas depletion timescales estimated from the model are consistent with the high-redshift SMGs in the literature within the uncertainties. We find no evidence of evolution of depletion time with redshift in SMGs at z > 3. This is the most detailed study of molecular gas content of a galaxy in the EoR to date, with the most distant detection of H 2 O in a galaxy without any evidence for active galactic nuclei in the literature.