We study non-perturbative aspects of QCD Kondo effect, which has been recently proposed for the finite density and strong magnetic field systems, using conformal field theory describing the low energy physics near the IR fixed point. We clarify the symmetry class of QCD Kondo effect both for the finite density and magnetic field systems, and show how the IR fixed point is non-perturbatively characterized by the boundary condition, which incorporates the impurity effect in Kondo problem. We also obtain the low temperature behavior of several quantities of QCD Kondo effect in the vicinity of the IR fixed point based on the conformal field theory analysis.