The physics of individual atmospheric vortices is far from clear, despite the fact that modern hydrodynamic models reliably reproduce them. In this paper, we develop the theory of vortices that stably exist for a long time in a certain region. Their structure is characterized by the first (dominant) empirical orthogonal function (EOF, NOF), and the dynamics is determined by the coefficient at a given mode y1(t), for which an ordinary differential equation is obtained based on the vorticity budget equation. The residual between the explicitly resolved terms is compensated by the parameterization, which is based on taking into account the effects of the second and subsequent modes of the EOF expansion. It is shown that it consists of Gaussian noise and a non-random component, which can be approximated using a cubic function of y1(t). To test the developed technique, we used modeling of the vorticity behavior describing the dynamics of the most stable vortex among all existing in the Earth’s atmosphere—the subtropical (Hawaiian) anticyclone. ERA5 reanalysis data were used for the work. The proposed approach to the analysis of integral vortex structures is supposed to be used to evaluate various circulation systems, identify factors affecting their dynamics in different regions, and study extreme hydrometeorological events associated with long-lived vortexes.