A novel poly(diallyldimethylammonium chloride) (PDDA) surface modified magnetic cobalt ferrite-filled multiwalled carbon nanotubes (CoFe2O4@MWCNTs-PDDA) composite is reported. The CoFe2O4@MWCNTs-PDDA was characterized by transmission electron microscopy, fourier transform infrared spectrometry, x-ray diffraction, and vibrating sample magnetometry and used for the selective adsorption of acidic proteins. The presence of MWCNTs served as a protective layer, which improved the stability of the magnetic composite, and also enlarged the surface area from 67 m2·g−1 to 186 m2·g−1, which provided a substrate with larger specific surface area for PDDA wrapping and enhanced the selectivity and adsorption capacity for acidic proteins. The adsorption capacity of CoFe2O4@MWCNTs-PDDA was 378.1 mg·g−1 for bovine serum albumin and 363.4 mg·g−1 for ovalbumin, an increase of approximately 20-fold, 3-fold, and 4-fold compared to CoFe2O4, CoFe2O4@PDDA and CoFe2O4@MWCNTs, respectively. The practical application of the CoFe2O4@MWCNTs-PDDA was demonstrated by processing whole blood samples for the extraction of acidic proteins. Satisfactory results were obtained by sodium dodecyl sulfate–polyacrylamide gel electrophoresis.