Breakup of droplets at bi-layer bifurcating junction in polydimethylsiloxane (PDMS) microchannel has been investigated by experiments and numerical simulation. The pressure drop in bi-layer bifurcating channel was investigated and compared with single-layer bifurcating channel. Daughter droplet size variation generated in bi-layer bifurcating microchannel was analyzed. The correlation was proposed to predict the transition between breakup and non-breakup conditions of droplets in bi-layer bifurcating channel using a phase diagram. In the non-breakup regime, droplets exiting port can be switched via tuning flow resistance by controlling radius of curvature, and or channel height ratio. Compared with single-layer bifurcating junction, 3-D cutting in diagonal direction from bi-layer bifurcating junction induces asymmetric fission to form daughter droplets with distinct sizes while each size has good monodispersity. Lower pressure drop is required in the new microsystem. The understanding of the droplet fission in the novel microstructure will enable more versatile control over the emulsion formation, fission and sorting. The model system can be developed to investigate the encapsulation and release kinetics of emulsion templated particles such as drug encapsulated microcapsules as they flow through complex porous media structures, such as blood capillaries or the porous tissue structures, which feature with bifurcating junctions.