The fluid mixing plays a crucial role in continuous flow chemical process. To enhance the mixing efficiency, a novel mixer was designed and constructed by adding ellipsoidal baffle in large scale Y-shaped mixer. The mixing performance in the mixers were studied by computational fluid dynamics (CFD) simulations and experimentally verified by the Villermaux/Dushman method. Furthermore, the mixer structure was optimized, and the flow characteristics of the fluid in the optimal mixer were investigated. The results indicated that the mixer can improve the mixing performance and reduce the pressure drop on the premise of ensuring high throughput by the secondary flow disturbance of ellipsoidal baffle. All the findings reported provide useful references for enhancement of mixing efficiency and reduction of pressure drop in a large scale mixer.