This paper describes the preparation and application of methyldiethanolamine amination polychloromethyl styrene nanolatex (MDEAPL) and MDEAPL coated capillary column (ccc-MDEAPL). The ccc-MDEAPL column was characterized with steady EOF values from −14.6 × 10−5 to −19.8 × 10−5 at pH 7.08–7.56. A method using tetraazacalix[2]arene[2]triazine-modified silica gel (NCS) as solid-phase extraction (SPE) sorbent was developed for concentrating and purifying the two phytohormones, indole-3-acetic acid (IAA) and beta-indolebutyric acid (IBA) of different plants. The determination conditions of IAA and IBA for field-amplified sample stacking open-tubular capillary electrochromatography based on SPE with NCS sorbent (NCS-SPE-FASS-OT-CEC) were optimized as follows: background electrolyte, 30 mmol L−1 Tris + 24 mmol L−1 HClO4 (30 % acetonitrile, pH 7.24); ccc-MDEAPL, 50 μm i.d. × 50 cm (effective length 41.5 cm); separation voltage, −25 kV; column temperature, 25 °C; UV detection wavelength, 230 nm; water-plug injection, 30 mbar × 20 s; sample electrokinetic injection, −20 kV × 20 s. Under the optimized conditions, IAA and IBA were well separated within 6 min (Rs > 1.5). The NCS-SPE-FASS-OT-CEC method was validated in terms of linearity, sensitivity, selectivity, precision and accuracy. The detection limits were 8 ng mL−1 for IAA and 25 ng mL−1 for IBA (S/N = 3), respectively. The overall recoveries ranged from 81.0 to 89.0 %. The developed method was successfully applied for the determination of IAA and IBA in different positions of various plants.