Application of polymer as thickener of precursor solution for preparing boron nitride (BN) nanofibers by electrospinning brings carbon impurity in the nitride products. The control and removal of the carbon impurity are a key step in the synthesis of the BN nanofibers. In this article, the control and removal of the carbon impurity are well realized by introducing O2 and NH3 simultaneously. The carbon content in the BN nanofibers can be well controlled by changing O2/NH3 ratio, temperature, time, and gas flow rate. The effects of the carbon impurity on the structure of the BN products are investigated systematically.