Source-specific health risks of PM2.5-bound metals were analyzed for emission control by integrating source apportionment with health risk assessments of residents affected via inhalation pathways. A total of 218 daily PM2.5 samples were collected in 2016 in the central urban district of Beijing, China. Analyses showed that the mean annual concentrations of total heavy metals (THMs) and PM2.5 were 0.39 and 104.37 μg m−3, respectively. The heating season had significantly higher concentrations of THMs and PM2.5 (0.61, 134 μg m−3) than the non-heating season (0.27, 88.1 μg m−3) (p < 0.05). Among all metals, arsenic had the largest incremental cancer risk of 7.04 × 10−6. Six sources were identified by positive matrix factorization combined with conditional probability function and potential source contribution function analyses. The order of contribution to PM2.5-bound metal concentrations was resuspended dust (61.0%), traffic emission (16.3%), Cu-related industry (14.1%), coal combustion (3.7%), Cr-related industry (3.4%), and fuel oil combustion (1.6%). During the heating season, the contribution of coal combustion decreased slightly, which may have been due to the countermeasure of substituting coal for gas or electric heat in 2016. However, in terms of cancer risk contribution, coal combustion was the top contributor in both heating (3.5 × 10−6, 51.6%) and non-heating (2.7 × 10−6, 59.6%) seasons due to high attributable contents of the toxic metals, As, Cd and Pb. The Cr-related and Cu-related industries were the next controlled sources in the heating and non-heating seasons, respectively. Thus, these sources should receive priority in the development of control measures. Display omitted •Individual PM2.5-bound heavy metals have higher concentrations in heating season.•Arsenic had the largest cancer risk, exceeding the acceptable level (1 × 10−6).•Six identical sources with seasonal contribution order were found by PMF-CPF-PSCF.•Resuspended dust contributed the greatest mass concentration.•With the highest cancer risk, coal combustion should be the priority control objective.