The carbon matrix in cell walls of lignocellulosic plants has high recalcitrance to chemical and biological decomposition. Thermal treatments, such as torrefaction and pyrolysis are therefore of interest to pre-process biomass. Reed canary grass (RCG) as biomass model was treated at 90, 300, 400 and 500°C in N2 atmosphere. The induced cell wall changes, especially for C and Ca and their speciation and nanomapping were studied using synchrotron based (1) scanning transmission X-ray microscopy (STXM) C 1s near edge X-ray absorption fine structure (NEXAFS) spectroscopy, (2) STXM Ca K-edge NEXAFS, and (3) Ca K-edge X-ray absorption of near edge structure (XANES) spectroscopy.Clusters of nano-based pixels having different spectral features were identified using principal component analysis of mosaics of C 1s NEXAFS images. At 300°C there were only minor changes and peaks related to lignin were only slight reduced. At 400°C, the chemical change was substantial and most resonances related to CO and CH functional groups declined considerably. Finally, at 500°C there were two clusters indicating that the structural integrity of the cell wall was lost and aromatic CC resonances related to quinones appeared. These results were confirmed by FT-IR. The nanomapping also indicated that Ca oxalate has a sub-micron particle size distribution, most sizes <200nm. These may act as seed particles during combustion. Ca speciation according to Ca K-edge XANES showed that oxalate (CaC2O4) was the primary phase of Ca and thermal treatment induced minor Ca phase transition into butschliite (K2Ca(CO3)2) and hydroxyapatite (Ca5(PO4)3OH).