Recently amylose has drawn much attention as a potential vehicle for the nanoencapsulation of different flavor molecules, and the encapsulation efficiency of the complex is an important index for the evaluation of its embedding effect. In this study, three different methods for assessing encapsulation efficiency of amylose-flavor complexes were compared. We chose heptanol and menthone as the flavor molecules, as both of them exhibit a typical odor. The complexes were prepared by the melting method, and their structures were characterized by XRD. In addition, the encapsulation efficiency was determined by thermal gravimetric analysis (TGA), potentiometric titration (PT), and headspace solid phase microextraction gas chromatography (HS-SPME-GC), respectively. The results showed that PT results were within the reported literature range while HS-SPME-GC seemed to overestimate the results and TGA results were the lowest. What is more, the operations of TGA and PT were relatively simple and the results were reproducible, while the HS-SPME-GC method displayed excellent high sensitivity. Therefore, PT method is the best method for assessing encapsulation efficiency of amylose-flavor complexes.