The extractives in wood have been proved to have some effect on the permeability and adhesive quality of the waterborne coating. Due to the hydrophobic property of extractives, water in aqueous coatings does not easily enter the wood cell wall, which affects the performance of the waterborne coating. Herein, a nanoindentation 3D mapping experiment was performed on the bonding areas between the waterborne coating, extractive-free wood and control wood, respectively. The variability of the reduced elastic modulus (E-r) and the hardness (H) was evaluated for an area of 100 mu m by 100 mu m. Overall, theE(r)andHof the waterborne coating were different from the values of wood. It demonstrated that the extraction procedure had a negative impact on theE(r)andHof the waterborne coating. The average values ofE(r)andHof the coating area were both higher when coated on the control wood sample surface (E-r: 2.836 GPa,H: 0.105 GPa) than on the extractive-free one (E-r: 2.390 GPa,H: 0.079 GPa). However, the average values ofE(r)andHin the wood increased by 50.43% and 33.67% after extraction, respectively. This study will help to understand the adhesion mechanism of the interface between the waterborne coating and the wood.