Background Renal calculi remain a major economic and health burden worldwide and are considered a systemic disorder associated with multiple other diseases. Several studies have observed that patients with idiopathic calcium renal stones show a reduction in bone mass. This study aimed to evaluate bone mass reduction on a non-contrast CT scan study in a group of idiopathic calcium-containing renal calculus disease patients in comparison with subjects without renal calculus disease. Methodology This non-interventional, cross-sectional study included a total of 300 patients with 150 cases (with renal calculi) and 150 controls (without renal calculi). Patients were divided according to age groups of 18-40, 40-60, and more than 60 years. The renal calculus size and the mean iliac bone thickness were calculated, and Spearman’s correlation test was used to determine the correlation between them. Results The mean iliac bone thickness was significantly lower in the cases (3.29 mm) compared to the controls (9.73 mm with a standard deviation of 1.341 mm). There was a statistically significant negative correlation between the size of the renal calculus and the mean iliac bone thickness. Conclusions Renal calculus disease associated with hypercalciuria caused by increased bone resorption is reflected by the decreased iliac bone thickness on CT scans. Our study used the iliac bone (cancellous bone) in predicting bone mass reduction which shows changes early in the course of the disease compared to the neck of the femur and lumbar vertebrae (compact bones). It helps in predicting osteoporosis early and prevents the progression of the disease through early and appropriate clinical and urological intervention.