Phosphorylated cellulose nanocrystals (P-CNCs) are a superior alternative to conventional sulfuric acid-derived CNCs because of their enhanced thermal and colloidal stability. However, further research is needed to understand the factors influencing their synthesis and properties for advanced material applications. In this study, P-CNCs were synthesized from bleached hardwood kraft pulp (BEKP) using a controlled hydrolysis method involving pretreatment with H3PO4 followed by reaction with metaphosphoric acid (HPO3) and urea. To optimize the process, a full factorial design was employed to evaluate the effects of reaction time (60–90 min) and HPO3 concentration (3–4 M). The P-CNCs were characterized using physicochemical, morphological, and thermal analyses. Surface charge densities ranged from 757 to 1993 mmol/kg, with exceptional colloidal stability, as evidenced by zeta potentials ranging from −30.17 to −67.40 mV. Statistical analysis showed that reaction time had a significant main effect on surface charge (p-value = 0.0022) and zeta potential (p-value = 0.0448), while a significant interaction between reaction time and HPO3 concentration was observed when analyzing the surface charge (p-value = 0.0097), suggesting a combined effect of these factors on the surface modification of CNC. Crystallinity indices ranged from 63.6% to 71.3%, and the thermal stability exceeded that of the raw material. These findings contribute to a better understanding of the surface modification and stability of P-CNCs and support efforts to sustainably produce functional CNCs for advanced composite applications.