Complex interactions between cellulose molecules and small molecules can lead to dramatic changes in the structure of the hydrogen bond network in cellulose in green sustainable deep eutectic solvents (DESs). However, the molecular and ionic evolution mechanism of DESs on cellulose nanofibrillation is still unclear. In this study, the mechanism and the critical role of action of ions in DESs on cellulose nanofibrillation were investigated. The results showed that cellulose nanofiber (CNF) with a diameter of less than 200 nm can be prepared directly by DES containing lactic acid (LA) and chloride (LA/ammonium chloride (NH4Cl) and LA/dodecyltrimethylammonium chloride (DTAC) with a diameter of less than 200 nm, and LA/zinc chloride (ZnCl2) with a diameter of less than 100 nm). The Kamlet-Abboud-Taft parameters (KAT value) showed that DESs containing LA have higher hydrogen bond acidity (α) than other systems (such as ethylene glycol and urea) without LA, which can provide more active protons to improve the proton mobility in the cellulose nanofibrillation. And DESs composed of LA and Cl− have high hydrogen bond alkalinity (β), which can lead to great changes in the original hydrogen bond network of cellulose and form a new hydrogen bond structure, thus making the deconstruction of cellulose easy. Thus, LA can be esterified with hydroxyl groups of cellulose under high-temperature moistening conditions, and the CNF prepared by DES system containing LA and Cl− had a highest degree of substitution (DS) (up to 0.73 in LA/ZnCl2 system) after high-temperature moistening.