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As a major city is often the core of a region, its inner spatial economic relationships may be a cause of larger regional disparities in economic development. However, empirical studies of the impact of uneven economic development within the inner city are rare compared to the extensive research conducted for states, provinces, and countries. This paper compares the intra-city spatial economic relationships in Shanghai with those in Beijing using Exploratory Spatial Data Analysis (ESDA). It concludes that Beijing exhibits negative spatial autocorrelation as the economic inequalities are accentuated among its 18 districts, leading to a center-concentrated pattern of development. In contrast, Shanghai shows positive spatial autocorrelation as the 17 districts in the city have synergistically benefitted from its economic growth. Moreover, the agglomeration effect in Shanghai is estimated to be higher than that in Beijing.