Non-equilibrium elemental doping is important for realizing high-content doping and combining elements with low miscibility. The elemental doping mechanism and kinetics of metal oxide nanoparticles (MOx NPs) are crucial for the design and precise control of the doping process; however, it has not yet been established. Herein, using organic-modified Mn-doped CeO2 NPs as a model material, a time-resolved investigation was conducted under subcritical/supercritical conditions to elucidate the doping mechanism. Owing to the intensified mass and heat transfer in the continuous flow system, rapid reaction startup and quenching were easily achieved, enabling the intermediates to be captured at times ranging from milliseconds to minutes. The Mn doping content was very high initially and decreased with increasing crystallite size (under subcritical condition, residence time: 0.2 s → 70.1 s, crystallite size: 3.1 nm → 5.3 nm, Mn doping content: 9.8 % → 3.9 %). The particle size and structure effects were further corroborated by analyzing the elemental distribution in small and large particles using high-resolution energy-dispersive spectrometry elemental mapping. The smaller particles exhibited a higher Mn doping content than the larger grown particles. Besides the kinetic effect, process conditions also play a significant role. Transitioning from a thermodynamically non-equilibrium to equilibrium state within tens of seconds, the solubility of Mn in CeO2 NPs is simultaneously determined by kinetic and thermodynamic factors, including growth time, temperature and solvent/solute properties. These findings, along with the flow synthesis strategy, lay the groundwork for incorporating immiscible or low-miscible elements into the same MOx NPs, tailoring their properties for various real-world applications.