The citizenization of migrant agricultural population is an important way to promote the new urbanization. There may be differences in the willingness and capacity of citizenization of migrant agricultural population with different employment status. Based on the dynamic monitoring data of floating population of the National Bureau of Statistics in 2016, this study took 48 cities in the Yangtze River Delta, Pearl River Delta and Beijing-Tianjin-Hebei as research samples, and used the Logistics regression model and propensity score matching (PSM) method to analyze the citizenization willingness and capacity of self-employed and employed migrant agricultural population under different city sizes. It is found that: (1) There exists a differentiation between the willingness and capacity of self-employed and employed migrant agricultural population to become citizens in cities of different sizes; (2) In super megacities and megacities, the citizenization willingness of self-employed migrant agricultural population is significantly stronger than that of employed migrant agricultural population, but in medium-sized and small cities, their citizenization willingness is significantly weaker than that of employed migrant agricultural population; (3) In megacities, the citizenization capacity of self-employed migrant agricultural population is significantly lower than that of employed migrant agricultural population, but in large, medium-sized, and small cities, the citizenization capacity of self-employed migrant agricultural population is significantly higher than that of employed migrant agricultural population. Governments should implement differential policies considering employment status and optimize the allocation of human resources. In super megacities and megacities, governments should give priority to promoting the citizenization of self-employed migrant agricultural population. In medium-sized and small cities, governments should give priority to boosting the citizenization of employed migrant agricultural population. In large cities, the citizenization of both self-employed and employed migrant agricultural population should be considered.