The scientific field of two-dimensional (2D) nanostructures has witnessed tremendous development during the last decade. To date, different synthesis approaches have been developed; therefore, various exceptional properties of this family of advanced materials have been discovered. It has recently been found that the natural surface oxide films of room-temperature liquid metals is an emerging platform for the synthesis of novel types of 2D nanostructures with numerous functional applications. However, most of the developed synthesis techniques for these materials are based on the direct mechanical exfoliation of 2D materials as research targets. This paper reports a facile and functional sonochemical-assisted approach for the synthesis of 2D hybrid and complex multilayered nanostructures with tunable characteristics. In this method, the intense interaction of acoustic waves with microfluidic gallium-based room-temperature liquid galinstan alloy provides the activation energy for synthesis of hybrid 2D nanostructures. The microstructural characterizations reveal the impact of sonochemical synthesis parameters, including the processing time and composition of the ionic synthesis environment, on the growth of GaxOy/Se 2D hybrid structures and InGaxOy/Se multilayered crystalline structures with tunable photonic characteristics. This technique shows promising potential for synthesis of various types of 2D and layered semiconductor nanostructures with tunable photonic characteristics.