Protein enrichment and separation is one of the pivotal preliminary steps of proteomics studies, which is important to medical diagnosis and treatment. In this study, procion brilliant blue-doped silica nanorod was prepared via self-assembly sol-gel technology without any additional template. Procion brilliant blue was covalently linked to 3-aminopropyltriethyloxy silane in ethanol. Tetraethylorthosilane (TEOS) was then added into the mixture, subsequently hydrolyzed and co-condensed for 3 h under stirring. The resulted nanorods were isolated by centrifugation, re-dispersed in deionized water, and centrifuged again. This wash process was repeated three times. Finally, the nanorods were dried under vacuum. Procion brilliant blue acted simultaneously as a self-assembly template during the preparation process, and subsequently as recognition probe for proteins. Scanning electron microscopy (SEM) image showed that the nanotubes were 2-16 microm in length and 200-500 nm in diameter. The obtained nanorods were further characterized by Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) and differential scanning calorimetry (DSA), separately. All these results indicated that procion brilliant blue were successfully doped into silica nanorods. The recognition property of nanorods for bovine serum albumin (BSA) was investigated under static condition. The resulted nanorods showed high binding capacity (57.6 mg/g) for BSA and fast adsorption equilibrium (within 60 min). The nanorods were also evaluated with four typical proteins, hemoglobin, trypsin, lysozyme and pepsin, with different relative molecular masses and isoelectric points. The results indicated that the prepared nanorods exhibited the highest binding capacity for trypsin (87.5 mg/g) and the least binding for hemoglobin (Hb, 3.0 mg/g). This easy preparation protocol and excellent recognition property make the prepared materials a bright future in proteomics research.