The aim of the work was to study the features of autonomic regulation of heart rhythm (HR) in women in the peri- and postmenopausal periods, depending on morphofunctional asymmetries of the female body. A total of 417 women aged 35–60 were examined. According to the lateral behavioral profile of asymmetries of the female body (Annette’s test), the nature of vegetative regulation at rest and orthostasis was determined according to the data of cardiac intervalography using the Varicard 2.51 complex and the Eskim-6 program. As a result, it was found that in the reproductive period in women with the right lateral phenotype, the autonomous circuit of HR variability regulation prevailed, and in ambidextrous women, the central one dominated. Ambidextrous and right-handers were characterized by egalitarian modulation, while left-handers were characterized by a respiratory typology of autonomic regulation of HR. In perimenopause, a moderate tension of regulatory mechanisms was formed in the lateral subgroups, and a high tension was formed in the postmenopausal subgroups. In ambidextrous and left-handers, discoordination of HR regulation prevailed. Thus, women with the polarity of the lateral phenotype in the late reproductive period were distinguished by the stability and economy of the mechanisms of autonomic regulation of HR. Ambidextrous had the most energy-consuming mechanisms in the postmenopausal period, which is a risk of cardiovascular disease pathology.