Objective Our study was to analyze the drug resistance spectrum, drug resistance sites, and clinical characteristics of children with drug-resistant tuberculosis (DR-TB) in Chongqing. Methods A total of 296 Mycobacterium tuberculosis (MTB) strains were isolated from pediatric patients of Children's Hospital of Chongqing Medical University from January 2014 to December 2022. These isolates were tested for anti-TB drugs with phenotypic drug susceptibility test (DST), and their potential genotypic resistance mutations were identified with whole genome sequencing (WGS). The clinical characteristics of DR-TB patients were analyzed retrospectively. Results According to phenotypic DST, 17.2% (51/296) of the strains were DR-TB, and no new gene mutations associated with drug resistance were detected by WGS. There were 240 patients in the drug-sensitive group and 51 in the drug-resistant group. Compared with the drug-sensitive group, the proportion of female, retreatment, severe tuberculosis, pulmonary tuberculosis combined with extrapulmonary tuberculosis, second-line drug use, treatment failure or death was higher, but the BCG vaccination rate was lower in the drug-resistant group, and the differences were statistically significant (P<0.05). A total of 288 children completed chest CT examination. Compared with the drug-sensitive group, the drug-resistant group involved a higher proportion of both lungs, involved more lobes, more likely to involve the lower right lobe, and had a higher percentage of necrosis, and the differences were all statistically significant (P<0.05). Compared with the drug-sensitive group, the proportion of positive acid-fast staining smear ≥1 times was higher, and the positive rate of T-SPOT.TB was lower in the drug-resistant group, with statistical significance (P<0.05). Conclusions The proportion of DR-TB in children in Chongqing is relatively high, and the gene mutations associated with drug resistance are similar to those in adults. Female, retreatment, and no BCG vaccination may be associated with DR-TB. Children with DR-TB have a wider range of lung involvement, are more likely to experience lung necrosis, and have a higher risk of lung lesions spreading to extra-pulmonary organs and progressing to severe disease, with higher rates of treatment failure or death. The overall positive rate of pathogen detection was higher in DR-TB children, but the positive rate of immunological examination was lower, suggesting that the children may have immune suppression.