In this paper, an in-situ microfluidic control unit (MCU) was designed and applied in a hydrothermal synthesis process, which provides an easy way to localize liquid-phase reaction and realize selective synthesis and direct growth of nanostructures as well as their morphology, all in a low-temperature and atmospheric environment. The morphology was controlled through controlling the amount of additivities using the MCU. This achieved a facile fabrication of Al doped ZnO (AZO) nanoflakes vertically grown on flexible polymer substrates with enhanced light scattering and dye loading capabilities. Flexible DSSCs with a significant enhancement (410% compare to ZnO NRs based devices) in power conversion efficiency were obtained using AZO nanoflake photoanodes of 6 μm thick, due to the enhancement in electron mobility and reduction in recombination. This hydrothermal synthesis using the in-situ MCU provides an efficient and scalable technique to synthesize controllable nanostructures with characteristics of easy set-up, low energy consumption and low cost.