A molecular beam mass spectrometry system for in situ measurement of the concentration of gas phase species including radicals impinging on a substrate during thermal plasma chemical vapor deposition (TPCVD) has been designed and constructed. Dynamically controlled substrate temperature was achieved using a variable thermal contact resistance method via a backside flow of an argon/helium mixture. A high quality molecular beam with beam-to-background signal greater than 20 was obtained under film growth conditions by sampling through a small nozzle (75 mum) in the center of the substrate. Mass discrimination effects were accounted for in order to quantify the species measurements. We demonstrate that this system has a minimum detection limit of under 100 ppb. Quantitative measurements of hydrocarbon species (H, H-2, C, CH3, CH4, C2H2, C2H4) using Ar/H-2/ CH4 mixtures and silicon species (Si, SiH, SiH2, SiCl, SiCl2, Cl, HCl) using Ar/ H-2/SiCl4 mixtures were obtained under thermal plasma chemical vapor deposition conditions.