As the life of the International Space Station (ISS) is lengthening, Russian crews are dominated by cosmonauts over 40 years of age who have repeatedly made a space flight (SF) and have a long stay on the ISS. In order to study the age-related features of the regulation of heart rate variability (HRV) in cosmonauts, based on proteomics data, we analyzed simultaneously the obtained data on the proteomic composition of urine samples and electrocardiogram (ECG) parameters, followed by an analysis of heart rate variability (HRV) in cosmonauts in the age group of 46,5+/-3,4 (n=12). The survey was carried out in the period of preparation for the next flight. The urine proteome was studied by mass spectrometry and analyzed by bioinformatic methods. Heart rate variability was assessed by software methods for analyzing ECG fragments. For the first time, data based on proteomics on the age-related features of the regulation of heart rate variability in cosmonauts are presented. According to age periodization, cosmonauts are in the middle age of the second period. The concentrations of mucin 1, type VI collagen, and cadherin 13 were shown to change with age. A decrease in HRV was also observed with increasing age. There was an increase in sympathetic influence and a progressive decrease in parasympathetic influence.