Beijing/W lineage strains of Mycobacterium tuberculosis spread faster than other strains, tend to be more virulent and frequently associated with drug resistance. In this study, to distinguish the characteristics of Beijing/W lineage and non-Beijing/W lineage M. tuberculosis, we assessed the growth between the two groups under conditions of hypoxia, nutrient starvation, and intracellular growth in murine macrophages. We also examined the DNA, RNA, and protein levels of 5 major M. tuberculosis proteins, including HspX, Hsp65, 38 kDa, Ag85B, and MPT64 of the different types of strains by sequencing, quantitative RT-PCR, and Western blotting. The results showed that Beijing/W and non-Beijing/W lineage strains of M. tuberculosis have similar viability in ex vivo culture but differ in their ability to survive within macrophages, and the intracellular viability of the Beijing/W lineage strains was significantly more than the viability of the non-Beijing/W lineage strains at 2, 3, and 5 days after infection (P < 0.05). Psts1 and fbpB were expressed at statistically lower levels in Beijing/W lineage strains in their mRNA expression levels (P < 0.05). The expression of their corresponding 38 kDa and Ag85B was lower in the Beijing/W lineage strains than the non-Beijing/W lineage strains (P < 0.05). The expression of HspX and Hsp65 was higher in the Beijing/W lineage strains in their protein expression levels at 24 h after infection of RAW264.7 macrophages (P < 0.05). In conclusion, the increased viability of the Beijing/W lineage strains might be related to the expression levels of these proteins.