Surface modification of carbon nanotubes is crucial for the dispersion and interfacial adhesion of carbon nanotubes in polymer composites. Here we present a novel method to construct single-walled carbon nanotube/chitosan composites using phosphotungstic acid as an anchor reagent to modify single-walled carbon nanotubes. The most direct benefit from this method is that this modification is mild but effective: the induced defects on single-walled carbon nanotubes are negligible based on Raman and transmission electron microscopy observations; and homogeneous dispersion of single-walled carbon nanotubes in chitosan matrices and strong binding between single-walled carbon nanotubes and chitosan are achieved. Moreover, according to the results of tetrazolium-based colorimetric assays in vitro, we demonstrate that the produced phosphotungstic-acid-modified single-walled carbon nanotube/chitosan composites have good biocompatibility. Thus, our study provides a feasible route to fabricate biocompatible composites containing single-walled carbon nanotubes for potential application in bone tissue engineering.