Hydroxymethylfurfural (HMF) is one of the compounds formed due to the heat treatment and storage of honey. The maximum level of HMF in honey has been set at 40 ppm under codex standards. In this study, the effects of heating temperature (55, 65 and 75°C), heating time (10, 20 and 30 min) as well as storage temperature (25 and 40°C) were assayed during the three months of storage based on response surface methodology (RSM). The effect of the above-mentioned variables on physicochemical properties (Lab color factors, pH and moisture) and the samples' HMF content (based on spectrophotometric technique) was studied. The prediction model of each treatment was calculated. The outcomes during the 45 and 90 days of storage were analyzed. Results showed that temperature, time of heat treatment and storage duration did not affect pH, moisture content and color; while storage temperature had a significant effect on L^* and a^*. HMF content was affected by all the variables, so its rate increased significantly with increasing thermal process and storage time. Among the studied samples, HMF content exceeded the standard limit in the sample heated at 75°C for 20 min and kept at 40°C for 90 days. The optimal level of HMF resulted by heating at 55°C for 10 min and under the storage temperature of 25°C for 45 days.