Obesity has been linked to vitamin D (VD) deficiency and low calcium (CAL) status. In the last decade, dietary supplementation of vitamin D and calcium (VD–CAL) have been extensively studied in animal experiments and human studies. However, the physiological mechanisms remain unknown as to whether the VD–CAL axis improves homeostasis and reduces biomarkers in regulating obesity and other metabolic diseases directly or indirectly. This review sought to investigate their connections. This topic was examined in scientific databases such as Web of Science, Scopus, and PubMed from 2011 to 2021, and 87 articles were generated for interpretation. Mechanistically, VD–CAL regulates from the organs to the blood, influencing insulin, lipids, hormone, cell, and inflammatory functions in obesity and its comorbidities, such as non-alcoholic fatty liver disease, cardiovascular disease, and type-2 diabetes mellitus. Nevertheless, previous research has not consistently shown that simultaneous VD–CAL supplementation affects weight loss or reduces fat content. This discrepancy may be influenced by population age and diversity, ethnicity, and geographical location, and also by degree of obesity and applied doses. Therefore, a larger prospective cohort and randomised trials are needed to determine the exact role of VD–CAL and their interrelationship.