Joule heating is an undesirable effect in capillary electrophoresis (CE). The heat generated by the electrical current leads to a temperature gradient along the separation channel and consequently affects the separation quality. Since the heat is inversely proportional to the electric resistance of the separation column, increasing the electric resistance can reduce the effect of Joule heating. Currently, due to the limit of fabrication technique and detection apparatus, the typical dimensions of CE microchannels are in the range of 50 μm to 200 μm. In this paper, we describe the method of reducing the cross-sectional area of the separation channel and increasing the channel’s surface for better heat dissipation. A photonic crystal fiber (PCF) is a bundle of extremely narrow channels, which ideally work as separation columns. The PCF was simply encapsulated in a polymethylmethacrylate (PMMA) microchannel right after a T-shaped injector. CE was simultaneously but independently carried out in 54 narrow capillaries, each capillary with diameter of 3.7 μm. The capillary bundle could sustain high electric field strength up to 1000 V/cm due to efficient heat dissipation, thus faster and enhanced separation was attained.