To evaluate the effects of processing steps in honey production on physicochemical properties and phenolic profile, the processing treatments of preheating (45/50/55 °C, 30 min), filtration (100/150/200 mesh) and moisture reduction (45/50/55 °C, 20 min, 0.09 MPa) were performed on rape honey (Brassica napus). The results showed that there was a significant decrease in the diastase activity during preheating and a significant increase in the 5-hydroxymethylfurfural content during moisture reduction. As for ten phenolic compounds determined in this study using high-performance liquid chromatography coupled with electrochemical detection (HPLC-ECD), the process of moisture reduction with the temperature of 55 °C led to the most significant decrease in the content of phenolics. Compared with phenolic acids, thermal treatments had less effect on flavonoids. The concentrations of pollen grains enriched with phenolics reduced from 2.36 ± 0.11 to 0.46 ± 0.10 pollen grains·mm−2 after the process of filtration. Thus, the results indicated that the decrease of pollen concentrations caused by filtration and the temperature change during thermal treatments were considered to be the factors affecting the content of phenolic compounds. Taken together, even the mild processing treatments of honey may decrease the potential functional components and thus affecting the intrinsic quality of honey.