Focusing on the changing roles of organizations, this study develops an institutional framework to examine the shifting stratification order since the mid-1990s in urban China. We argue that, after the mid-1990s, the Chinese state led a dual process of institutional transformation. On the one hand, the state dismantled the socialist redistributive system and broke down institutional segmentation based on organizational ownership and bureaucratic rank. On the other hand, the state developed different markets with various paces and strategies, resulting in fragmented market environments. In this context, reformed organizations interacted with heterogeneous market conditions to exert different impacts on multiple dimensions of social inequality. We draw empirical evidence from two national survey data collected in 1994 and 2003 during a critical period. Our findings show that the foundation of the stratification order has shifted from institutional segmentation to market fragmentation in urban China. This study calls for substantive institutional analysis to better understand the intricate landscape of social inequality in transitional economies.