Liquid hot water (LHW) pretreatment is an effective method to improve enzymatic digestibility of lignocellulosic feedstock by removing hemicellulose/lignin. To better understand how LHW pretreatment reduces plant cell wall recalcitrance, we applied a combined approach using multiple microscopic techniques and chemometric methods to monitor microstructural and topochemical changes in the fiber cell wall of sugar maple (Acer saccharum). The heterogeneity of deconstruction in various cell wall layers was easily visualized based on chemical characterizations through confocal Raman microscopy, combining with principal component analysis and cluster analysis. Interestingly, after LHW pretreatment, the S2 layer was differentiated into two regions, namely a heavy-damaged region (outer and thin inner S2) with more polysaccharides removed, and a light-damaged region (middle S2) which still remained relatively intact. Our results have established a direct correlation between microstructural and topochemical changes of a cell wall following LHW pretreatment. The removal of polysaccharides (mainly hemicelluloses) rather than lignin played a critical role in the visible damage of the cell wall, like cavities, gaps and collapses.