In this work, we theoretically explore the characteristics of electroosmostic flow (EOF) in a microcavity with nonuniform surface charges. It is well known that a uniformly charged EOF does not give rise to flow separation because of its irrotational nature, as opposed to the classical problem of viscous flow past a cavity. However, if the cavity walls bear nonuniform surface charges, then the similitude between electric and flow fields breaks down, leading to the generation of vorticity in the cavity. Because this vorticity must necessarily diffuse into the exterior region that possesses a zero vorticity set by a uniform EOF, a new flow structure emerges. Assuming Stokes flow, we employ a boundary element method to explore how a nonuniform charge distribution along the cavity surface affects the flow structure. The results show that the stream can be susceptible to flow separation and exhibits a variety of flow structures, depending on the distributions of zeta potentials and the aspect ratio of the cavity. The interactions between patterned EOF vortices and Moffatt eddies are further demonstrated for deep cavities. This work not only has implications for electrokinetic flow induced by surface imperfections but also provides optimal strategies for achieving effective mixing in microgrooves.