Instead of extracting every selected harmonic component, the current reference of selective active power filter (APF) can be also obtained by filtering out the fundamental component from distorted load current for computation efficiency. This type of mixed current reference contains kinds of harmonic components and easily involves noises. In this condition, selective harmonic compensation must be realized by the current controller. With regard that selectivity is the most significant feature of controller, this paper presents specific comparison analysis between two types of resonant controllers: proportional-resonant (PR) controller and vector-resonant (VR) controller. The comparison analysis covers the relations, performances, and stability of both controllers. Analysis results conclude that the poorer selectivity of the PR controller could be relatively improved, but limitations from system stability make the improvement hardly realized. By contrast, the VR controller exhibits excellent selectivity and is more suitable for selective APF with mixed current reference. Experimental results from laboratory prototype validate the reasonability of analysis. And the features of each resonant controller are concluded.