Molybdenum disulfide is considered one of the most promising anodes for lithium-ion batteries due to its high specific capacity; however, it suffers from an unstable solid electrolyte interphase. Understanding its structural evolution and reaction mechanism upon charging/discharging is crucial for further improvements in battery performance. Herein, the interfacial processes of solid electrolyte interphase film formation and lithiation/delithiation on ultra-flat monolayer molybdenum disulfide are monitored by in situ atomic force microscopy. The live formation of ultra-thin and dense films can be induced by the use of fluoroethylene carbonate as an additive to effectively protect the anode electrodes. The evolution of the fluoroethylene carbonate-derived solid electrolyte interphase film upon cycling is quantitatively analysed. Furthermore, the formation of wrinkle-structure networks upon lithiation process is distinguished in detailed steps, and accordingly, structure-reactivity correlations are proposed. These quantitative results provide an in-depth understanding of the interfacial mechanism in molybdenum disulfide-based lithium-ion batteries.