The effect of dispersion compensating photonic crystal fiber (DC-PCF) on dual-channel photonic time-stretched analog-to-digital converter (PTS-ADC) is studied. The principle that DC-PCF can suppress third-order harmonic in PTS-ADC is theoretically verified. The dual-channel PTS-ADC based on DC-PCF is designed and simulated with the Optisystem software. The effective number of bits (ENOB) of PTS-ADC is simulated and compared between DC-PCF and dispersion compensation fiber (DCF) as dispersive mediums under the condition of five different input radio frequencies (RF) signals (16.25, 20.25, 24.25, 28.25, 32.25 GHz). The simulation results show that DC-PCF can effectively suppress the generation of third-order harmonics and improve the quantization resolution of dual channel PTS-ADC system.