In this study, we constructed the first global proteomic atlas of Kac, Khib, and Kma modifications in developing cassava roots, identifying 11,253 Kac, 18,326 Khib, and 4,068 Kma sites across 5,165, 4,832, and 1,815 proteins, respectively. Comparative sequence analysis revealed conservation of Kac and Khib sites in histones across cassava, sugarcane, and rice, with higher sequence conservation observed in histone H2A and H4 compared to H2B. Functional enrichment demonstrated that PTM-modified proteins were predominantly involved in sucrose/starch metabolism, glycolysis/gluconeogenesis, pentose phosphate pathway, TCA cycle, pyruvate metabolism, and lignin biosynthesis, with the majority exhibiting multiple PTM co-occurrence. In addition, hundreds of modified proteins associated with stress response, hormone metabolism, and transcription factors were also identified, of which a few proteins displayed significant type-specific modification preferences.