5-hydroxymethyl-2-furaldehyde (5-HMF) is an important substance that affect quality of honey and shows toxicity for humans and honey bees. The pathway of 5-HMF formation in honey is still unknown. In this study, we tested the effect of thermal treatment (at 90 °C for 4 h) on the formulation of 5-HMF formulation in rapeseed with varied honey composition. 5-HMF content of honey increased at higher water content, Ca²⁺ and Mg²⁺ content and lower pH. However, the formation of 5-HMF was not significantly influenced by glucose, fructose, Na⁺, or K⁺ contents. Furthermore, different content of proline, the most abundant amino acid in honey (a substance in Maillard reaction), had no effect on 5-HMF formation. Free acids in honey can catalyze fructose and glucose to form 5-HMF. These results suggest that dehydration of glucose or fructose, instead of the Maillard reaction, is the main pathway of 5-HMF formation in honey. This study gives new insights for the mechanisms of 5-HMF formation and provides method for reducing 5-HMF formation during honey processing.