Tuberculosis (TB) is the leading cause of death caused by single pathogenic microorganism, Mycobacterium tuberculosis (MTB). The study aims to explore the associations of microRNA (miRNA) single-nucleotide polymorphisms (SNPs) with pulmonary TB (PTB) risk. A population-based case−control study was conducted, and 168 newly diagnosed smear-positive PTB cases and 251 non-TB controls were recruited. SNPs located within miR-27a (rs895819), miR-423 (rs6505162), miR-196a-2 (rs11614913), miR-146a (rs2910164), miR-618 (rs2682818) were selected and MassARRAY® MALDI-TOF System was employed for genotyping. SPSS19.0 was adopted for statistical analysis, non-conditional logistic regression was performed. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were computed to estimate the associations. Associations of haplotypes with PTB risk were performed with online tool. Rs895819 CT/CC genotype was associated with reduced PTB risk among female population (OR = 0.45, 95% CI: 0.23–0.98), P = 0.045. Haplotypes (combined with rs895819, rs2682818, rs2910164, rs6505162 and rs11614913) TCCCT, TAGCC, CCCCC, CCGCT and TCGAT were associated with reduced PTB risk and the ORs were 0.67 (95% CI: 0.45–0.99), 0.49 (0.25–0.94), 0.34 (95% CI: 0.14–0.81), 0.22 (95% CI: 0.06–0.84) and 0.24 (95% CI: 0.07–0.79), respectively; while the haplotypes of TAGCT, CCCCT, CACCT and TCCAT were associated with increased PTB risk, and the ORs were 3.63 (95% CI: 1.54–8.55), 2.20 (95% CI: 1.00–4.86), 3.90 (95% CI: 1.47–10.36) and 2.95 (95% CI: 1.09–7.99), respectively. Rs895819 CT/CC genotype was associated with reduced female PTB risk and haplotype TCCCT, TAGCC, CCCCC, CCGCT and TCGAT were associated with reduced PTB risk, while TAGCT, CCCCT, CACCT and TCCAT were associated with increased risk.