Head-down bed rest (HDBR) is one of the models of the physiological effects of weightlessness used, among other things, to assess the effect of hypokinesia on the physiological systems of the human body and, first of all, on the cardiovascular system. The aim of the work was to study the effect of 21-day HDBR factors on the cardiovascular system based on blood proteomic profile data and myocardial stress biomarkers sST2, NT-proBNP, and the thrombogenesis risk marker D-dimer. It was revealed that HDBR conditions led to an increase in the level of proteins of the complement and the coagulation cascade systems, platelet degranulation, fibrinolysis, acute phase proteins, post-translational modification of proteins, retinol-binding protein 4 (RBP4), apolipoprotein B, S100A8, associated with cardiovascular diseases, and other proteins that affect the functions of endothelial cells. It has been shown that the level of proteins in the blood involved in the remodeling of the cytoskeleton, oxygen transport, heme catabolism, etc. decreased during HDBR. A significant decrease in the levels of NT-proBNP and sST2 by the 21st day of HDBR and a rapid recovery of their levels already on the first day of the rehabilitation period was established, which indicated the restoration of hemodynamic parameters of the heart function. The levels of D-dimer in different periods of the experiment and after its completion (on the 14th day) did not differ from the background values, which indicated the absence of the risk of thrombosis during this exposure and within 14 days after its completion.