The housing price in cities is affected by many factors. Due to the differences of economic development level, geographical conditions, cultural background and other factors in different cities in the same region, the housing price in different cities presents obvious differences. The housing price of urban agglomeration in the Pearl River Delta shows obvious stratification. By stratifying the housing price of nine cities in the Pearl River Delta, this paper selects certain economic indicators to analyze the factors affecting the housing price of each city. The results show that per capita disposable income and population density have a greater impact on the housing price of each tier of cities, while per capita GDP, population urbanization rate, real estate development investment, completed area of housing construction and other factors have different impacts on the housing price of different tiers cities.