In this paper, we present a highly effective microfluidic emulsion system using an integrated microchannel plate (MCP), a porous glass membrane that is readily available and densely packs millions of through-microchannels, for high-throughput production of monodisperse droplets. The physical controls of droplet formation, including viscosity, flow rate, and pore size, have been extensively explored for optimum emulsification conditions. The performance of the device has been validated where monodisperse droplets with a narrow coefficient of variance (<5%) can be achieved at a dispersed phase flux of 3 mL h-1 from a piece of 4 × 4 mm2 MCP. The average droplet size is two times the nominal membrane pore diameter and thus can be easily controlled by choosing the appropriate membrane type. The preparation of hydrogel microspheres has also been demonstrated with a high throughput of 1.5 × 106 particles min-1. These microspheres with a uniform size range and rough surface morphology provide suitable bioenvironments and serve as ideal carriers for cell culture. Mouse fibroblasts are shown to be cultured on these 3D scaffolds with an average cell viability of over 96%. The cell attachment rate can reach up to 112 ± 7% in 24 h and the proliferation ability increases with the number of culture days. Furthermore, the device has been applied in the droplet digital polymerase chain reaction for absolute quantification of lung cancer-related PLAU genes. The detection limit achieved was noted to be 0.5 copies/μL with a dynamic range of 105 ranging from 1 × 102 to 1 × 106 copies/μL. Given the easy fabrication, robust performance, and simple operation, the emulsion system sets the stage for the laboratory's droplet-based assays and applications in tissue engineering.