Although the smoking rate of human immunodeficiency virus (HIV), hepatitis B virus (HBV) or hepatitis C virus (HCV) infected people was much higher than that of the general population, smoking cessation interventions have long been ineffective. We aimed to examine the estimates of prevalence, time-trend, and association of smoking among people living with HIV, HBV, or HCV. This cohort was composed of 32,115 individuals from the NHANES database (1999–2018) and they were collected in the US. The time trend analysis of smoking and quitting rates was conducted using different years of survey follow-up and different infected groups. Multivariable logistic regression analysis was used to identify the risk factors related to smoking behavior of these infected people. Compared to non-infected smokers, infected smokers were more likely to be older (aged 30–39, OR = 9.92, CI 6.07–16.21; aged 40–49,OR = 3.51, CI 2.49–4.94), males (1.99, 1.54–2.55), lower education and economic level (1.78, 1.39–2.29; 2.05, 1.59–2.65), unemployed (1.63, 1.21–2.20), suffering depression (1.35, 1.05–1.72), and drug users (7.65, 5.04–11.59). Taken together, our study showed that these complex psychosocial characteristics and unhealthy behavioral factors might be major independent risk factors for increasing smoking rate and decreasing smoking cessation rate among these infected people.