Colored mutants of Porphyra haitanensis have superior production and quality characteristics, with two mutants, Shengfu 1 (SF-1) and Shengfu 2 (SF-2), having good high-temperature tolerances. To understand the molecular aspects of high-temperature tolerance, this study comprehensively investigated the metabolic differences between the high-temperature tolerant strains and wild type. Nuclear magnetic resonance (NMR) methods identified 35 algal metabolites, including sugars, amino acids, carboxylic acids, aldehydes, amines, and nucleotides. The results indicated that the high-temperature tolerant strains had significantly different metabolic phenotypes from the wild type. The high-temperature tolerant mutants had significantly higher levels in a set of osmolytes consisting of betaine, taurine, laminitol, and isofloridoside than the wild type, indicating the particular importance of efficient osmoregulation for high-temperature resistance. These findings provided essential metabolic information about high-temperature adaptation for P. haitanensis and demonstrated NMR-based metabolomics as a useful tool for understanding the metabolic features related to resistance to stressors.