Abstract: Main impurity in vacuum arc deuterium ion source (VADIS) was discussed and the formation of protium, as impurity in VADIS, and its influence on the quality of ion source beam were analyzed emphatically. The emission spectrums of VADIS worked at pulse and low-repeated frequency modes were measured using spectrum diagnosis, and the extraction beam of ion source was analyzed with D(d,n)~3He nuclear reaction too. The experimental results show that, protium, the most light hydrogen isotope, is the main impurity in VADIS, and impacts on the characters of VADIS seriously. And then, some advices are propounded to reduce the harm.