Protein is one of the main components in algal biomass and would be degraded into undesired N-heterocyclic compounds or amides during its thermal-chemical conversion. Hydrothermal pre-treatment (HTP) might remove part of N from raw material and therefore improve quality of bio-oil and solid residue. In this work, a low temperature HTP process was performed on high-protein Chlorella sp. and Bacillariophyta sp., and their depolymerization behaviour under different conditions (120-225℃, 5-60 min) was investigated. Special attention was paid on transfer behavior of nutrient nitrogen and organic carbon during HTP process. Functional structure and thermal-degradation behaviour of the obtained solid residue were intensively characterized through various techniques. Results showed that temperature played the most important role during HTP process. A large fraction of nitrogen was enriched into aqueous phase at elevated temperature due to hydrolysis of protein and deamination of amino acids, while more carbon were also detected in aqueous phase because of decarboxylation. The FTIR and XPS analysis indicated the appearance of pyridine-N in solid residue apart from protein-N and pyrrolidine-N. TG-FTIR-MS analysis combining with Py-GC/MS detection revealed that thermal degradation, evolution behavior of volatiles and products distribution from solid residue were greatly distinguished from those from raw material. This study will supply useful information for better thermal utilization of high-protein algae.