Selective separation of plant metabolite by encapsulated XAD-7 with poly-L-lysine membrane was analyzed in order to evaluate the design parameters in the in situ bioproduct separation. Encapsulated XAD-7 could selectively concentrate the berberine from dilute aqueous mixtures of berberine and dopamine which are target secondary metabolites and undesired intermediate metabolites of Thalictrum rugosum plant cell culture, respectively, though competitive adsorption of berberine and dopamine was observed. The selectivity of berberine adsorption on encapsulated XAD-7 was controlled by pH variation of medium based on pKa value of metabolites. A mathematical model using local thermodynamic equilibrium isotherm for competitive adsorption of berberine and dopamine on encapsulated XAD-7 was proposed to quantify the adsorption and to evaluate design parameters. The predicted concentration by the proposed model agreed reasonably well with the experimental measurement in competitive adsorption of berberine and dopamine on encapsulated XAD-7. The effects of various design parameters on selective adsorption in the in situ product separation process were evaluated based on the proposed model and thus the volume ratio of single capsule to total capsules was the most effective parameter to increase the selectivity of berberine on encapsulated XAD-7.