Gold nanochannels were prepared using Al2 O3 nanotubules membrane as the carrier and modified with chitosan by a classical N-(3-dimethylaminopropyl)-N-ethyl carbodiimide ( EDC)/N-hydroxysuccinimide ( NHS ) coupling reaction. The nanochannels were characterized by field emission scanning electron microscopy ( FESEM) , cyclic voltammetry and AC impedance method. The Au nanochannels modified with chitosan showed a chiral environment and can be used to separate histidine enantiomer. The effects of pore size and solution pH on the separation efficiency of histidine were investigated. To increase the detection sensitivity of D-, L-histidine, Ag nanoparticles were used to enhance the surface enhanced Raman scattering ( SERS) activity. The results showed that the chitosan-modified gold nanochannels can be used to separate chiral histidine based on this unique selective nanochannel membrane. L-Histidine and D-histidine were respectively detected by SERS at wavelengths of 1000 and 1590 cm-1 . The results showed that L-histidine and D-histidine were separated well in the mixture containing 200 μL of histidine, 100 μL of colloidal Ag and 100 μL of 80 mmol/L NaCl ( pH=7 . 59 ) with a separation efficiency of 4 . 91 .