Skeletal tuberculosis (STB) is one of the most common forms of extrapulmonary tuberculosis; however, limited epidemiological data are available on this public health concern worldwide, especially in developing countries. The aims of this study were to analyze the epidemiological characteristics of STB cases and to identify risk factors associated with drug resistance among STB cases in China. We included STB inpatients at Beijing Chest Hospital from January 2009 through December 2018. The multiple demographic and clinical variables of patients were collected from the hospital’s electronic patient record. In total, 3086 STB patients were hospitalized in Beijing Chest Hospital. Of these cases, 1988 (64.4%) were spinal TB cases, 991 (32.1%) were joint TB cases, and 107 (3.5%) were concurrent spinal-joint TB cases. The most frequent localization of the infections in joints included the knee (21.5%), hip (17.9%), and elbow (10.3%). For spinal TB, lumbar, thoracic, and cervical spinal TB were present in 51.7%, 40.6%, and 4.4% of cases, respectively. Positive cultures were reported in only 16.0% of STB cases. When patients aged ≥ 60 years old were used as the control group, youths (< 18 years old) were less likely to have spinal TB (aOR, 0.29; 95% CI, 0.21–0.41). The prevalence of MDR-TB was 12.5% among the STB cases, and more female cases were afflicted with drug-resistant STB than with drug-susceptible STB (aOR, 0.50; 95% CI, 0.27–0.94). In addition, patients aged < 18 years had significantly higher odds of having drug-resistant STB compared with those aged ≥ 60 years (aOR, 20.778; 95% CI, 4.49–96.149). In conclusion, our data demonstrate that spinal TB is the most frequent form of STB in China. The youths are less likely to have spinal TB compared with elderly patients, while the patients aged < 18 years have significantly higher odds of having drug-resistant STB than elderly patients.