Neuromodulation has made great strides in recent years, but in vitro studies have been limited to two-dimensional cell cultures, far from in vivo conditions. In this study, we realized a novel thermoplasmonic platform for modulating the neural activity of three-dimensional cell cultures, providing a new tool to bring in vitro neuromodulation studies into a three-dimensional environment. The photosensitive scaffold, obtained by covering soda-lime glass microbeads (diameter about 40 µm) with gold nanorods, integrates microbeads’ structural properties, intended to support the development of the neural network in three dimensions, with the photothermal properties of plasmonic nanoparticles. We demonstrate its efficiency in providing support for the construction of three-dimensional cell culture and how, under Near-infrared laser irradiation, their photothermal effect can precisely and non-invasively modulate the activity of the neural network. Our platform is expected to be a useful tool for improving neural network studies to better understand complex brain functions and neural disorders.