As hybrid nanomaterials have myriad of applications in modern technology, different functionalization strategies are being intensely sought for preparing nanocomposites with tunable properties and structures. Multi-Walled Carbon Nanotube (MWNT)/CdSe Quantum Dot (QD) heterostructures serve as an important example for an active component of solar cells. The attachment mechanism of CdSe QDs and MWNTs is known to affect the charge transfer between them and consequently to alter the efficiency of solar cell devices. In this study, we present a novel method that enables the exchange of some of the organic capping agents on the QDs with carboxyl functionalized MWNTs upon ultrasonication. This produces a ligand-free covalent attachment of the QDs to the MWNTs. EXAFS characterization reveals direct bond formation between the CdSe QDs and the MWNTs. The amount of oleic acid exchanged is quantified by temperature-programmed decomposition; the results indicate that roughly half of the oleic acid is removed from the QDs upon functionalized MWNT addition. Additionally, we characterize the optical and structural properties of the QD-MWNT heterostructures and investigate how these properties are affected by the attachment. The steady state photoluminescence response of QDs is completely quenched. The lifetime of the PL of the QDs measured with time resolved photoluminescence shows a significant decrease after they are covalently bonded to functionalized MWNTs, suggesting a fast charge transfer between QDs and MWNTs. Our theoretical calculations are consistent with and support these experimental findings and provide microscopic models for the QD binding mechanisms.