To understand the mechanisms responsible for thermal decomposition of a Zr-MOF (MIL-140C), we perform atomistic-scale molecular dynamics (MD) simulations and discuss the simulation data in comparison with the TEM images obtained for the decomposed Zr-MOF. First, we introduce the ReaxFF parameters suitable for the Zr/C/H/O chemistry and then apply them to investigate the thermal stability and morphological changes in the MIL-140C during heating. Based on the performed simulations we propose an atomic mechanism for the collapse of the MIL-140C and the molecular pathways for carbon monoxide formation, the main product of the MIL-140C thermal degradation. We also determine that the oxidation state of the ZrOx clusters, evolved due to the thermal degradation, approximates the tetragonal phase of ZrO2. Both simulations and experiments show a distribution of very small ZrOx clusters embedded in the disrupted organic sheet that could contribute to the unusual high catalytic activity of the decomposed MIL-140C.