Many studies revealed the rapid decline of atmospheric PM2.5 in Beijing due to the emission control measures. The variation of particle number concentration (PN) which has important influences on regional climate and human health, however, was rarely reported. This study measured the particle number size distributions (PNSD) in 3–700 nm in winter of Beijing during 2013–2019. It was found that PN decreased by 58% from 2013 to 2017, but increased by 29% from 2017 to 2019. By Positive matrix factorization (PMF) analysis, five source factors of PNSD were identified as Nucleation, Fresh traffic, Aged traffic + Diesel, Coal + biomass burning and Secondary. Overall, factors associated with primary emissions were found to decrease continuously. Coal + biomass burning dominated the reduction (65%) among the three primary sources during 2013–2017, which resulted from the great efforts on emission control of coal combustion and biomass burning. Fresh traffic and Aged traffic + Diesel decreased by 43% and 66%, respectively, from 2013 to 2019, as a result of the upgrade of the vehicle emission standards in Beijing-Tianjin-Hebei area. On the other hand, the contribution from Nucleation and Secondary decreased with the reduction of gaseous precursors in 2013–2017, but due to the increased intensity of new particle formation (NPF) and secondary oxidation, they increased by 56% and 70%, respectively, from 2017 to 2019, which led to the simultaneously increase of PN and particle volume concentration. This study indicated that NPF may play an important role in urban atmosphere under continuous air quality improvement.