A new system of multi-channel single-output joint fractional Fourier transform correlator (JFRTC) for color pattern recognition is proposed based on the conventional system of multi-channel single-output joint transform correlator (JTC). The theoretical analysis and optical experiments are performed. With this method, one can obtain three correlation peaks at the output plane which show a pair of desired cross-correlation peaks and one auto-correlation peak. In comparison, the conventional system leads to more correlation peaks playing a noise role in color pattern recognition.