The Atacama Large (Sub-)millimeter Array (ALMA) has provided glimpse of the interstellar medium (ISM) properties of galaxies at the Epoch of Reionization (EoR); however, detailed understanding of their internal structure is still lacking. We present properties of molecular cloud complexes (MCCs) in a prototypical galaxy at this epoch studied in cosmological zoom-in simulations (Leung et al. <xref rid="r8" ref-type="bibr">2019</xref>c). Typical MCC mass and size are comparable to nearby spirals and starburst galaxies (Mgas∼106.5M⊙ and R≃45-100 pc). MCCs are highly supersonic, with velocity dispersion of σgas≃20-100 km s-1 and pressure of P/kB ≃107.6Kcm-3, which are comparable to gas-rich starburst galaxies. In addition, we perform stability analysis to understand the origin and dynamical properties of MCCs. We find that MCCs are globally stable in the main disk of Althæa. Densest regions where star formation is expected to take place in clumps and cores on even smaller scales instead have lower virial parameter and Toomre-Q values. Detailed studies of the star-forming gas dynamics at the EoR thus require a spatial resolution of < 40 pc ( ≃ 0.01″), which is within reach of ALMA, to complement studies of stellar populations at EoR using the James Webb Space Telescope (JWST).