In this paper, we present a novel design of bilayer polydimethylsiloxane (PDMS) microchannel formed by bifurcated junction, from which each curved branch lies on the upper and lower layer, respectively. With this 3D platform, we aim to investigate droplet formation and subsequent fission in a multiphase system using non-Newtonian fluids, which are ubiquitous in daily life and have been widely used in industrial applications including biomedical engineering, food production, personal care and cosmetics, and material synthesis. Numerical model has been established to characterize the non-Newtonian effect to droplet fission and associated breakup dynamics when droplet flows through 3D bifurcated junction, where droplets can deform significantly on account of the confining geometric boundaries, and the flow of the surrounding non-Newtonian liquid, both of which control the deformation and breakup of each mother droplet into two daughter droplets. Dispersions of sodium carboxymethyl cellulose in water, and dispersions of polyvinylchloride in dioctylphthalate have been used as model fluids in the study, with the former one possessing shearthinning behaviour, while the latter one possessing shearthickening behaviour. The understanding of the droplet fission in the novel microstructure will enable more versatile control over the emulsion formation when non-Newtonian fluids are involved. The model systems in the study can be further developed to investigate the mechanical property of emulsion templated particles such as drug encapsulated microcapsules when they flow through complex media structures, such as blood capillaries or the porous tissue structure, which feature with bifurcated junction.