This study reports a microfluidic system for high throughput, uniform, and size-tunable generation of cell-containing collagen microbeads. The principle is based on two pneumatically-driven mechanisms to achieve multi-channel mixture suspension transportation, and to actuate the spotting actions of micro-vibrators that continuously generate tiny collagen micro-droplets into a thin oil layer and then a sterile Pluronic® F127 surfactant solution located below. The temporarily formed collagen microdroplets are then thermally gelatinized. By regulating the feeding rate of cells/collagen suspension, and the spotting frequency of micro-vibrator, the size of the collagen microbeads can be manipulated. One of the key technical features is its capability to generate uniform collagen microbeads (coefficient of variation: 5.4-8.6 %) with sizes ranging from 73.9 to 349.3 μm in diameter. This is currently difficult to achieve using the existing methods particularly the generation of cell-encapsulating collagen microbeads with diameter less than 100 μm. Another advantageous trait is that the ultrastructure of the generated collagen microbeads is similar to that found in native collagen. In this study, moreover, the use of the proposed device for the microencapsulation of 3T3 cells in collagen microbeads has been successfully demonstrated showing that the encapsulated cells maintained high cell viability (96 ± 2 %). Furthermore, a reasonable proliferative capability of the encapsulated cells was observed during 7 days culture. As a whole, the proposed device has opened up a new route to generate cell-containing collagen microbeads, which is found particularly meaningful for biomedical applications.