Chitosan (CS) based nanofibrous membranes were fabricated via hybrid electrospinning of chitosan (CS) and poly(epsilon-caprolactone) (PCL) or poly(epsilon-caprolactone)-block-poly(ethylene glycol) (PCL-b-PEG) copolymers for the adsorption of dyes from aqueous solution. The amphiphilic block polymers were obtained by polymerization of PCL and different molecular weights of PEG. It was observed that the secondary fiber and core-shell structure could be controlled by PEG segments. The results of XPS showed that as the molecular weight of the PEG segments increased, the content of CS on the fiber surface increased. The parameters of adsorption time, initial concentration and pH values on the adsorption capacity were studied. The adsorption experiments showed that the adsorption process toward Congo red (CR) on CS-based membranes fitted well with the pseudo-second-order model and Langmuir isotherm model. The CS-based membranes with PEG molecular weight of 5 kDa possessed good reusability and the maximum adsorption capacity calculated from the Langmuir model was 291.55 mg g(-1). The existence of intermolecular hydrogen bonds between CS and PCL-b-PEG copolymer reduced the loss of CS. Therefore, CS-based membranes would be promising materials for water remediation.