The effects of whey protein isolate (WPI)-pectin pre-emulsified vegetable oil on the physicochemical properties and microstructure of low-fat yogurt (LFY) were investigated by particle size distribution, water-holding capacity (WHC), texture, rheology, electron microscopy, storage stability, and sensory analysis. The vegetable oil was pre-emulsified into two types of emulsions, a mixed emulsion (ME: WPI-pectin complexes were adsorbed directly at the interface) and a bilayer emulsion (BE: Pectin was added to a previously established WPI-stabilized interface). The results showed that yogurts added with pre-emulsified vegetable oil (ME-Y, BE-Y) had significantly better quality than LFY, with better WHC, textural properties, rheological properties, and storage stability. The average particle size of ME (11.96µm) was larger than that of BE (10.23µm). The consistency of yogurt added with ME (ME-Y) was significantly higher than that of yogurt added with BE (BE-Y), at 2359.10 and 2181.12gs, respectively. Meanwhile, ME-Y exhibited storage stability similar to full-fat control (FFY) and higher sensory scores. Interestingly, the WHC of BE-Y (49.03%) was higher than that of ME-Y (45.63%). In addition, WPI+Pectin-Y exhibited higher WHC (53.81%) and consistency (2518.73gs) compared to ME-Y and BE-Y, but the particle size distribution was not uniform, and the direct addition of WPI, pectin, and oil had no positive effect on improving the rheological properties of yogurt. Overall, the addition of WPI-pectin pre-emulsified vegetable oil improved the quality of LFY. These findings are particularly relevant for the production of higher quality LFY.