In recent years, the demand for using more precise 3D cell models in physiology for research and drug discovery has been steadily increasing. Researchers have been building and maintaining various 3D cell models to study more diseases and physiological mechanisms [1,2]. Now we have the ability to overcome some limiting factors and complete complex experiments through faster and simpler operations, especially for precious samples separated from patients. The formation, processing, and staining of cell spheres and organoids are usually complex procedures that can easily cause sample damage or loss. In addition, high connotation imaging also poses certain challenges, as organoids tend to grow at the edges of the pores or be located at different positions and heights within the pores. And when conducting drug treatment and analysis in porous plates, the readings of each pore are limited. New technologies are rapidly developing to simplify and promote process improvement. We used the microfluidic device Pu · MA System 3D MAG and 3D flowchips (Protein Fluidics), along with a magnetic coated 3D cell model, to complete the automated experimental process (Figure 1). 3D cell model coated with magnetic nanoparticles in NanoShuttle ™ [3] , transferred into the hole and positioned in the center of the hole by a magnet embedded in the fluid chip. Automated microfluidic systems can achieve automatic replacement of culture media, addition of compounds, and treatment of microstructures. Then, the ImageXpress Micro Confocal High Content Imaging System (Molecular Devices) was used to capture high-resolution 3D structures and advanced analysis software was used to quantify the morphology of cell spheroids and organoids, as well as the effects of compounds.