The thermal stabilities of MOF-S and its methyl-modified structures were investigated using molecular dynamics (MD) simulations. Implementing reactive force field (ReaxFF) enabled the modeling of bond breakage during the high-temperature decomposition process. Thermal decomposition was initialized by the breakage of the weak coordination bond, followed by structural collapse at elevated temperatures. Deterioration of the thermal stability upon functionalization of the linker with methyl groups was observed and all the structures showed a negative thermal expansion behavior with the negative thermal trend augmented with increasing the number of methyl functional groups on the linker. The present work sheds light on the role that linker motion plays in lowering the thermal stability and also shows that the selection of a rigid linker can help improve the thermal stability of metal-organic frameworks for high-temperature applications.