A novel graphene/polystyrene composite electrode was developed for the enhanced amperometric detection of CE in this work. The composite electrode was fabricated on the basis of the in situ polymerization of a mixture of graphene and prepolymerized styrene in the bore of a piece of fused-silica capillary under heat. SEM, XRD, and FTIR offered insights into the nature of the composite. The results indicated that graphenes were well dispersed and embedded throughout the PS matrix to form an interconnected conducting network. The performance of this unique graphene-based detector has been demonstrated by separating and detecting rutin, isoquercitrin, quercitrin, and chlorogenic acid in Herba Houttuyniae (a traditional Chinese medicine) in combination with CE. The prepared graphene-based CE detector offered significantly lower detection potential, yielded enhanced signal-to-noise characteristics, and exhibited high resistance to surface fouling and enhanced stability. It showed long-term stability and reproducibility with a relative standard deviation of 3.1% for the peak current (n = 15).