Here we report on a generalized transport theory that leads to spatial patterns of intracellular organelles (101-103 nm) inside biological cells. To overcome the diffusion barrier of the crowded intracellular environment, cells utilize directed movements, powered by molecular motors, on cytoskeletal filaments to transport organelles from one part of the cell to another. Thus, at the operational level, the spatial distribution of organelles is controlled by activities of motor proteins, which are globally regulated by elaborate biochemical networks. In other words, a specific organization of organelles is a “signature” of complex interactions between many motors, organelles, and cytoskeletal filaments. Numerous experimental studies have been performed to explore the biochemical and physical aspects of organelle transport, however, a global, quantitative relationship between spatial patterns of organelles (the effect) and motor activities (the cause) are not to be found in the literature. In this work, we report a generalized theory based on diffusion-reaction-advection equations to establish the cause-effect relationships of spatial organelle patterns. We show that all organelle patterns in nature can be characterized by two dimensionless parameters, the one- and two-dimensional Peclet numbers. A regime map of distinct organelle patterns is then constructed and compared to a broad range of experimental observations. This study provides a firm theoretical ground for further studies of intracellular transport phenomena.