In this work, a new set of parton distribution functions taking into account the intrinsic charm (IC) contribution is presented. We focus on the impact of the European Muon Collaboration (EMC) measurements on the large x charm structure function as the strongest evidence for the intrinsic charm when combined with the HERA, SLAC, and BCDMS data. The main goal of this paper is the simultaneous determination of the intrinsic charm probability Pcc¯/p and strong coupling αs. This allows us to study the interaction of these two quantities as well as the influence on the PDFs in the presence of IC contributions. By considering αs which can be fix or free parameter from our QCD analysis, we find that although there is not a significant change in the extracted central value of PDFs and their uncertainties, the obtained value of Pcc¯/p change by factor 7.8%. The extracted value of Pcc¯/p in the present QCD analysis is consistent with the recent reported upper limit of 1.93%, which is obtained for the first time from LHC measurements. We show the intrinsic charm probability is sensitive to the strong coupling constant and also the charm mass. The extracted value of the strong coupling constant αs(MZ2)=0.1191±0.0008 at NLO is in good agreement with the world average value and available theoretical models.