(1) Background: Isoniazid resistance in Mycobacterium tuberculosis is primarily mediated by mutations in katG and inhA genes, yet the molecular characteristics of coding region mutations and their clinical correlations in Vietnamese patients remain incompletely understood; (2) Methods: We conducted a cross-sectional study analyzing exon mutations in katG and inhA genes using Sanger sequencing in 56 isoniazid-resistant pulmonary tuberculosis patients treated at the National Lung Hospital from January 2023 to June 2024, with comprehensive clinical and paraclinical data collection; (3) Results: Exon mutations in katG were detected in 11 patients (19.6%) and inhA in 7 patients (12.5%), with no concurrent mutations. The Ser315Thr mutation was present in all katG-positive cases (100%), while all inhA mutations were concentrated in codon cluster 233-240 with 63/96 being amino acid-changing variants. Patients with katG or inhA mutations had significantly higher rates of pulmonary rales compared to those without mutations (90.9% and 85.7% vs. 34.2%, p < 0.001), and inhA mutations were exclusively found in multidrug-resistant tuberculosis cases (p = 0.012); (4) Conclusions: Our findings identify codon cluster 233-240 as a novel inhA mutation hotspot in Vietnamese strains and demonstrate significant associations between specific mutations and disease severity. The exclusive presence of inhA mutations in MDR-TB cases and the correlation between genotype and clinical manifestations support the implementation of genotype-guided diagnostic and therapeutic strategies for isoniazid-resistant tuberculosis.