Carbonized polymer dots (CPDs) have emerged as a fascinating class of functional nanomaterials with unique physicochemical properties. However, the mechanisms governing their formation and photoluminescence remain a subject of intense debate. In this study, we conducted a systematic comparison of the structural, morphological, and optical properties of CPDs synthesized using various methods, revealing the self-assembly characteristics of low-molecular-weight CPDs with relatively complex structures. Through comprehensive structural, morphological, and optical analyses, we found that CPDs with fewer endogenous derivatives exhibited pronounced concentration-dependent self-assembly, leading to larger particle sizes and enhanced fluorescence emission at higher concentrations. In contrast, CPDs with higher proportions of endogenous derivatives showed limited self-assembly due to complex supramolecular interactions between the derivatives and polymer chains. Remarkably, the removal of endogenous derivatives using a ternary solvent extraction method significantly enhanced the self-assembly and fluorescence of the CPDs. These findings highlight the critical role of endogenous derivatives in modulating the self-assembly and photophysical properties of CPDs, paving the way for future advancements in this field.