Electrolyte ionic diffusivity significantly affects the power density and useable energy density of a lithium ion battery. During usage, electrolyte can decompose, leading to reduced ionic diffusivity. Understanding the degradation mechanism and its effect on ionic diffusivity is important for both battery design optimization to provide superior performance with a long cycle life and for better battery management during usage to extend the battery life. In this research, the ionic diffusivity of key electrolytes and their degradation, including DMC-LiPF6, EMC-LiPF6 and DEC-LiPF6, are quantitatively predicted with classical and ReaxFF molecular dynamics simulations. The electrolyte solvent structures and reaction pathways are characterized. The effect of temperature, salt concentration and degree of thermal degradation on electrolyte ionic diffusivity are identified. A list of gas-phase, solvent-phase and solid-phase degradation products are categorized. DMC-LiPF6 shows the highest thermal stability, while DEC-LiPF6 shows the lowest thermal stability because of a large amount of –CH3CH2 group in the molecule. PF 6 - tends to decompose first. The decomposed product of PF5 can further lead to C–O bond breaking in solvent molecules, causing them to decompose into products composed of smaller molecules. Simulations show that the diffusion coefficients of cations and anions decrease with thermal degradation. The mechanism is found to be related to the clustering of Li+, R-O- and (R–OCO2)-, which impedes ion diffusion in the electrolyte. This paper provides a quantitative understanding of electrolyte thermal degradation, revealing the underlying mechanisms and effects on electrolyte properties at the atomistic level by a systematic comparative study for the first time. The approach will provide valuable guidance to the development of lithium ion batteries.