The (3-aminopropyl)triethoxysilane (APTES) self-assembled monolayer (SAM) has been widely used in fundamental research and engineering applications; however, characterization of its surface wetting properties remains problematic. Surface wetting properties of the APTES SAM were systematically investigated using different contact angle measurement techniques. The observed unique nonideal wetting was related to the APTES SAM structure, including surface hydrogen bond formation, the surface roughness, and the effect of water penetration. The contact angle decreased dramatically with the residence time on the APTES SAM surface, and a special contact angle hysteresis phenomenon was observed. The contact angle could be distorted by the calculation method used for the nonideal APTES SAM surface. Values calculated by the tangent-leaning method were thought to be more accurate and credible. Our findings demonstrated that static advancing contact angles were the most stable and credible for characterizing the APTES SAM surface wettability.