Typical fabrication processes of compact silicon quantum dot (Si QD) devices or components entail several synthesis, processing and stabilization steps, leading to manufacture and cost inefficiency. Here we report a single step strategy through which nanoscale architectures based on Si QDs can be simultaneously synthesized and integrated in designated positions by using a femtosecond laser (532 nm wavelength and 200 fs pulse duration) direct writing technique. The extreme environments of a femtosecond laser focal spot can result in millisecond synthesis and integration of Si architectures stacked by Si QDs with a unique crystal structure (central hexagonal). This approach involves a three-photon absorption process that can obtain nanoscale Si architecture units with a narrow line width of 450 nm. These Si architectures exhibited bright luminescence peaked at 712 nm. Our strategy can fabricate Si micro/nano-architectures to tightly attach to a designated position in one step, which demonstrates great potential for fabricating active layers of integrated circuit components or other compact devices based on Si QDs.