A bare fused silica capillary lacks enough efficiency for electrophoretic separation under some circumstances as a complex mixture of analogous compounds or stroma matrix. To improve the separation, a strategy of functionalization for the inner surface with nano-silica and polyelectrolytes is proposed in this paper. The results have demonstrated that the hybrid coating film of poly(diallyldimethylammonium chloride) (PDDA)–nano-SiO₂–poly(styrenesulfonate) (PSS) on a silica capillary greatly promoted the separation efficiency. As a model, four analytes (naringenin, rutin, quercetin and ascorbic acid) are well separated with 24 mmol L⁻¹ borate buffer solution (pH 8.3) as the carrier. The proposed approach was successfully applied for rapid determination of these analytes in artificial urine with satisfactory results.