The present study characterized the morphology of fish oil b-cyclodextrin (b-CD) complex or fish oil encapsulated with polycaprolactone (PCL) by transmission electron microscopy (TEM) observation using low or high voltage with or without phosphotungstic acid (PTA) staining. Emulsion–diffusion or self-assembly aggregation methods were used to encapsulate fish oil in PCL or b-CD. PCL spheres averaged 200 nm in diameter. However, b-CD spheres were significantly larger and dependent on host:guest mixing ratio (w:w), being approximately 300 nm and 600 nm at ratios of 10:1 and 10:10, respectively. TEM enabled the visual distinction of core and wall materials, and revealed that fish oil was encapsulated with a different structure depending on whether the self-resembling aggregation of b-CD or emulsion–diffusion method with PCL was used. Hexagonal-type b-CD aggregates were evident at a mixing ratio 10:1 between b-CD and fish oil. The hexagonal arrangement of b-CD enveloped the fish oil with a thick (100–150 nm) membrane. Incorporation of b-CD with fish oil at a 10:10 mixing ratio produced a worm-type of b-CD. It is suggested that the fish oil might be physically blended without wrapping with b-CD. For the PCL formulation, the lower voltage TEM operating condition better enabled the observation of the thin PCL layer (1–2 nm) encapsulating the fish oil. Nanosizer and TEM yielded comparable measurements.