The investigation of the dispersion behavior of fluorinated MWCNTs (F-MWCNTs) is very important to understand their structure and take full advantage of their good properties. In this present paper, the dispersion behavior of F-MWCNTs with a low content and a high content of fluorine (denoted as lF-MWCNTs and hF-MWCNTs) was explored in 18 kinds of common solvents. The surface of hF-MWCNTs is considered to be a heterostructure consisting of fluorinated regions and aromatic regions, while lF-MWCNTs are inclined to be a homogeneous structure on the basis of their dispersion behavior. According to dispersion theory based on surface energy and Hansen solubility parameters (HSPs), it was indicated that the corresponding preferable solvents are different for different regions. As a result, good solvents of hF-MWCNTs are distributed in a quite wide scope while lF-MWCNTs can be dispersed only in a significantly narrow range of solvents. The HSPs of lF-MWCNTs and hF-MWCNTs are determined to be δD = 17.6 MPa1/2, δP = 11.8 MPa1/2, δH = 8.8 MPa1/2 and δD = 16.9 MPa1/2, δP = 9.3 MPa1/2, δH = 13.5 MPa1/2, respectively. As a result, mixed solvents of acetone and water were carefully tuned to be compatible with hF-MWCNTs. The dispersion behaviors of lF-MWCNTs and hF-MWCNTs in epoxy were also predicted according to HSPs. It was found that hF-MWCNTs maintain a stable dispersion in epoxy due to their heterogeneous structure at elevated temperatures.