Room temperature (RT) nanoimprinting is an attractive technique for nanofabrication, because it is not required a thermal cycle or UV irradiation process. Previously, it has reported that RT-nanoimprinting enables the fabrication of nanostructures using hydrogen silsesquioxane (HSQ) as a resin. HSQ has the HSiO 3/2 structure and transforms to SiO x , such as glass, upon annealing. We developed, for the first time, reversal nanoimprint using RT nanoimprint to fabricate a three-dimensional (3D) HSQ structure and succeeded in fabricating a 3D HSQ nanostructure with two crossstacked layers. Furthermore, it was confirmed that the 3D HSQ structure has a sufficient interface adhesion between the upper and lower layers by a durability test using ultrasonic vibration and also that it was not deformed after an annealing treatment at 1000 °C.