Multi-walled carbon nanotubes (MWCNTs) with special nanoneedle structure have emerged as new promising candidates for plasmid and drug delivery. However, the delivery is greatly limited by the high tendency of CNT to form aggregates, the "less dispersion problem," and CNT cytotoxicity. Here, we described an extensive evaluation of the ability of layer-by-layer modification strategy to reduce CNT size and toxicity, and to shield CNT hydrophobic surfaces. The MWCNTs can be derivatized with carboxylate groups (cMWCNT) and sequentially functionalized with protein, cationic polyethylenimine (PEI), and polysaccharide. The protein coating, characterized by Fourier transform infrared and deconvolution methods, could serve as the hydrophilic, biocompatible matrix and scaffold for sequential conjugation. We found that coated PEI-enhanced electrostatic interactions between plasmid DNA and CNTs. The functionalized cMWCNTs were analyzed by thermogravimetric analysis, dynamic light scattering, and electron microscopy technologies. The conjugation of cMWCNTs-ovalbumin-PEI with oxidized pectin further promoted green fluorescence intensity by balancing the intracellular DNA release and were easier to disperse. Our in-depth study demonstrated that functionalized CNTs can be improved by fine-tuned process parameters of the protein-PEI-polysaccharide modification.