Urban ecosystems evolve over time and space as the outcome of dynamic interactions between socio-economic and biophysical processes operating over multiple scales. The ecological resilience of urban ecosystems, the degree to which they tolerate alteration before reorganizing around a new set of structures and processes, is influenced by these interactions. In cities and urbanizing areas fragmentation of natural habitats, simplification and homogenization of species composition, disruption of hydrological systems, and alteration of energy flow and nutrient cycling reduce cross-scale resilience, leaving systems increasingly vulnerable to shifts in system control and structure. Because varied urban development patterns affect the amount and interspersion of built and natural land cover, as well as the human demands on ecosystems differently, we argue that alternative urban patterns (i.e., urban form, land use distribution, and connectivity) generate varied effects on ecosystem dynamics and their ecological resilience. We build on urban economics, landscape ecology, population dynamics, and complex system science to propose a conceptual model and a set of hypotheses that explicitly link urban pattern to human and ecosystem functions in urban ecosystems. We propose that resilience in urban ecosystems is a function of the patterns of human activities and natural habitats that control and are controlled by both socio-economic and biophysical processes operating at various scales. We discuss the implications of this conceptual model for urban planning and design.