The analysis of human physiological systems from the point of view of complex systems theory remains a very ambitious task. The complexity of the problem often encourages the use of innovative mathematical methods analyzing the processes that take place in space and time. The main goal of this paper is to visualize the cardiovascular system during auricular vagus nerve stimulation (aVNS) using the matrix differences to evaluate the dynamic signal interfaces by cointegrating the initial signal data into the matrices during each case. Algebraic relationships between RR/JT and JT/QRS cardiac intervals are used not only to track the cardiovascular changes during aVNS but also to characterize individual features of the person during the transit through the therapy. This paper presents the computational techniques that can visualize the complex dynamical processes taking place in the cardiovascular system using the electrical aVNS therapy. Four healthy volunteers participated in two verum and two placebo experiments. We discovered that the body’s reaction to the stimulation was very different in each of the cases, but the presented techniques opened new possibilities for a novel interpretation of the dynamics of the cardiovascular system.