Objective To explore the application value of gene chip method and linear probe method in detecting Mycobacterium tuberculosis (MTB) in sputum specimens. Methods 106 suspected pulmonary tuberculosis outpatients and inpatients in the Second Affiliated Hospital of Hainan Medical University in March-July 2018 were enrolled in the study, sputum specimens were detected by gene chip method and linear probe method, then compared with the modified Roche culture method; proportional susceptibility test was as gold standard to analyze the efficacy of above two methods in detection of rifampicin and isoniazid resistance. Results 106 sputum specimens were cultured by modified Roche culture method, positive rate was 52.83%(56/106), 46 specimens were identified as MTB positive. 46 and 53 strains of MTB were detected by gene chip method and linear probe method respectively, there was no significant difference in MTB detection results between gene chip method, linear probe method, and modified Roche culture method (all P>0.05). There was no significant difference but good consistency in detection of rifampicin resistance of MTB between gene chip method, linear probe method, and proportional method (all P>0.05, all Kappa>0.75). For rifampicin resistance detection, the sensitivity and specificity of gene chip method were 84.62% and 90.00% respectively, and the linear probe method were 84.62% and 85.00% respectively. There was no significant difference but general consistency in detection of isoniazid resistance of MTB between gene chip method, lin-ear probe method, and proportional method (all P>0.05, all Kappa<0.75). For isoniazid resistance detection, the sensitivity and specificity of gene chip method were 69.23% (18/26) and 95.00% (19/20) respectively, linear probe method were 65.38% (17/26) and 85.00% (17/20) respectively. Conclusion Both gene chip method and linear probe method can accurately and rapidly identify MTB from sputum specimens of most suspected tuberculosis patients, they can also be used for rapid detection of rifampicin and isoniazid resistance, thus guiding clinical antimicrobial use, which are worthy of clinical promotion.