Understanding and transforming how cities think is a crucial part of developing effective knowledge infrastructures for the Anthropocene. In this article, we review knowledge co-production as a popular approach in environmental and sustainability science communities to the generation of useable knowledge for sustainability and resilience. We present knowledge systems analysis as a conceptual and empirical framework for understanding existing co-production processes as preconditions to the design of new knowledge infrastructures in cities. Knowledge systems are the organizational practices and routines that make, validate, communicate, and apply knowledge. The knowledge systems analysis framework examines both the workings of these practices and routines and their interplay with the visions, values, social relations, and power dynamics embedded in the governance of building sustainable cities. The framework can be useful in uncovering hidden relations and highlighting the societal foundations that shape what is (and what is not) known by cities and how cities can co-produce new knowledge with meaningful sustainability and resilience actions and transformations. We highlight key innovations and design philosophies that we think can advance research and practice on knowledge co-production for urban sustainability and resilience.