A microwave aqueous synthesis method has been successfully utilized for preparing mesoporous carbon adsorbents, and the microwave aqueous treatment duration has been decreased from 10 h of hydrothermal treatment to less than 1 h. The mesoporous carbons have Brunauer–Emmett–Teller (BET) surface areas ranging from 1913.5 to 2213.8 m2/g, pore volumes from 1.41 to 2.40 cm3/g, average pore diameters between 3.29 and 4.40 nm, and the surfaces of the mesoporous carbons are mainly hydrophilic with few O-containing functional groups. The pore textural properties of the mesoporous carbons critically depend on the microwave treatment conditions. All the mesoporous carbons showed considerable adsorption ability for berberine hydrochloride and matrine, and the highest adsorption capacities at the initial concentration of 0.08 mg/mL and 298 K are 363.8 mg/g and 269.7 mg/g, respectively. Adsorption thermodynamic parameters of berberine hydrochloride and matrine on the selected carbon sample were calculated. The adsorption rate of the two alkaloids on the selected carbon sample is fast. These results indicate that the microwave-prepared mesoporous carbons could be promising adsorbents for highly efficient adsorption of berberine hydrochloride and matrine.