Hydrothermal pretreatment with characteristic of green chemistry is considered as promising technology in the biorefineries. Using material balance and multiscale characterization techniques, the effects of process severity factor and pH on chemical behaviors of lignin-carbohydrate complex (LCC) were systematically studied. During pretreatment, spatial relocation of lignin with covalently linked xylan facilitated local cell wall collapse. A kinetic model was established to describe the behaviors of LCC components changing with severity factor. It was found that cleavage of LCC linkage was strongly pH-dependent. Low pH dominated cleavage of coumarate/ferulate esters which cross-linking lignin with xylan and repolymerization of aromatics either from furfural or lignin into polymers such as pseudo lignin, while high pH which allowed the existence of soluble LCC dominated the aldol condensations from xylose to aromatics and depolymerizaton of lignin to phenols. Detailed reaction pathways concerned with LCC were finally established to elucidate the underlying mechanism. (c) 2018 American Institute of Chemical Engineers AIChE J, 64: 1938-1953, 2018