The spatial structure and efficiency is one part of the core content of Economic Geography. In recent years, based on the context of rapid development of metropolitan areas, some western scholars have been attempting to explore the relationship between spatial structure and labor productivity from the perspective of population aggregation effectiveness in metropolitan district. It is believed that the concentration can improve labor productivity. The paper measures the urban population spatial structure of administrative region of cities in the Northeast China by selecting 36 prefecture-level cities of Northeast China as samples, using data of the fifth national population census in 2000 and adopting the indicators of urban population polycentricity and decentrality which are offered by Meijers et al. In addition, the paper also has a derivation of demonstration regression model on the basis of OLS and Cobb-Douglas production function, and then takes a demonstration study on labor productivity and indicators such as polycentricity, decentrality and population scale of primate city. The objectives of this paper are generalized as: 1) to analyze the relationship between regional spatial structure and labor productivity; 2) to explore whether there is a similar relationship between structure and efficiency by comparing western researches conducted at the level of metropolitan areas with prefecture-level cities of Northeast China. The present study will undoubtedly provide a valuable theoretical basis for the prevalent regional urban systems planning in China. The main conclusions are drawn as follows: 1) The population scale of primate city has a positive correlation with labor productivity. In other words, larger population scale of primate city shows a higher labor productivity; 2) Polycentricity does not show higher labor productivity. There is no significant effect, no matter the spatial organization is single-center or multi-center, on labor productivity and also has not displayed the characteristics of scale dependence and space dependence; 3) Decentrality has an adverse impact on labor productivity, which is affected by population scale and area scale of administrative region of cities. More decentrality shows a lower labor productivity, and the population scale and area scale of administrative region of cities have a direct impact on the lower level of labor productivity when the decentrality is constant. Correspondingly, the spatial structure tending to concentration can lead to a higher labor productivity.