Borrowing cost-income theory, a micro decision-making mechanism model of agricultural population’s citizenization is designed in the perspective of the willingness of agricultural population’s citizenization and economic rationality, and according to the survey data of Chongqing, the empirical test is implemented. The research shows that there is positive correlation between the income of the migration population, social network, education level, agricultural production cost, rural house construction cost and the number of migration population；there is negative correlation between urban labor force quality, urban housing price, urban daily cost and the number of migration population. After the migration population is employed stably, decision of citizenization is made according to the cost and income of migration. Only if the income excesses the cost, the migration is implemented； if not, the migration population will go back to countryside. Therefore, only removing the barrier of registration system of the urban and rural areas cannot accelerate citizenization. In addition, the income of migration population should be added and the cost should be cut.