A novel and simple method for preparation of a tentacle-type polymer stationary phase grafted with polyethyleneimine (PEI) anion exchanger was developed for open tubular capillary electrochromatography (OT-CEC) of nucleosides and proteins. The polymeric stationary phase was prepared using 3-chloro-2-hydroxypropyl methacrylate (HPMA-Cl)-based reactive monomer. The preparation procedure included pretreatment of the capillary inner wall, silanization, in situ graft polymerization with HPMA-Cl and PEI modification. To compare with the tentacle-type capillary column with PEI functionalization, a monolayer capillary column without PEI functionalization was also prepared. The electrochromatographic characterization of the prepared open tubular column was performed using alkylbenzenes. The electroosmotic flow (EOF) with regard to PEI concentrations and the running buffer pH was investigated. The separation conditions of the nucleosides and the proteins were optimized. The modified tentacle-type column with high anion exchange capacity has proven to afford better retention and resolution for the separation of nucleosides and proteins. The PEI functionalization column can also provide long-term stable use for biomolecule separation using a single capillary with relative standard deviation values of retention times of less than 2%. The results indicate that the present method for open tubular capillary preparation with a HPMA-Cl-based reactive monomer is promising for OT-CEC biomolecule separation.