This paper summarizes the recent development of a portable self-contained system to unravel the intricate multiscale dynamical processes from real oceanic flows, which are in nature highly nonlinear and intermittent in space and time. Of particular focus are the interactions among largescale, mesoscale, and submesoscale processes.We firsu introduce the concept of scale window, and an orthogonal subspace decomposition technigue called multiscale window transform (MWT). Established on MWT is a rigorous formalism of multiscale transport, perfect transfer, and multiscale conversion, which makes a new methodology, multiscale energy and vorticity analysis (MS-EVA). A direct application of the MS-EVA is the development of a novel localized instability analysis, generalizing the classical notion of hydrodynamic instability to finite amplitude processes on irregularly variable domains. The theory is consistent with the analytical solutions of Eady’s model and Kuo’s model, the benchmark models of baroclinic instability and barotropic instability; it is further validated with a vortex shedding control problem. We have put it to application with a variety of complicated real ocean problems, which would be otherwise very difficult, if not impossible, to tackle. Briefly shown in this paper include the dynamical studies of a highly variable open ocean front, and a complex coastal ocean circulation. In the former, it is found that underlying the frontal meandering is a convective instability followed by an absolute instability, and correspondingly a rapid spatially amplifying mode locked into a temporally growing mode; in the latter, we see a real ocean example of how upwelling can be driven by winds through nonlinear instability, and how winds may excite the ocean via an avenue which is distinctly different from the classical paradigms. This system is mathematically rigorous, physically robust, and practically straightforward. This paper summarizes the recent development of a portable self-contained system to unravel the intricate multiscale dynamical processes from real oceanic flows, which are in nature highly nonlinear and intermittent in space and time. Of particular focus are the interactions among largescale, mesoscale, and submesoscale processes. We firsu introduce the concept of scale window, and an orthogonal subspace decomposition technigue called multiscale window transform (MWT). Established on MWT is a rigorous formalism of multiscale transport, perfect transfer, and multiscale conversion, which makes a new methodology, multiscale energy and vorticity analysis (MS-EVA). A direct application of the MS-EVA is the development of a novel localized instability analysis, generalizing the classical notion of hydrodynamic instability to finite amplitude processes on irregularly variable domains. The theory is consistent with the analytical solutions of Eady’s model and Kuo’s model, the benchmark models o we have put it to application with a variety of complicated real ocean problems, which would be otherwise very difficult, if not impossible, to tackle. Briefly shown in this paper include the dynamical studies of a highly variable open ocean front, and a complex coastal ocean circulation, a complex instability followed by an absolute instability, and correspondingly a rapid spatially amplifying mode locked into a temporally growing mode; in the latter, we see a real ocean example of how upwelling can be driven by winds through nonlinear instability, and how winds may excite the ocean via an avenue which is distinctly different from the classical paradigms. is mathematically rigorous, physically robust, and practically straightforward.