Molecular dynamics simulations were performed to study the embedding behavior on functionalized polypropylene surfaces with combined topographical and chemical anisotropies. Three different substrate structure types were constructed to give a periodic, non-polar, and hydrophobic functionality. The carboxyl thiol monolayer covered structure bottoms are polar and hydrophilic in nature. Both static wetting and dynamic impact of nano-sized water droplets together with temperature effect were considered. The results revealed unconventional wetting on the functionalized surfaces when comparing to the purely structured counterparts. Complete water embedding was achieved under suitable conditions varied with the substrate topography.