The microball end mills are widely used in the processing of micro parts in the fields of aerospace. These micro parts are often made of hard to machine materials with high hardness and strength, such as martensitic stainless steel. As the main processing tool of these parts, the micro cutting tools wear fast and have a short service life. At the same time, because of the small diameter and complex structure of the micro ball end milling tool, its preparation process is complex, and its quality is difficult to guarantee. In order to solve the above problems, a micro ball end milling tool with a flat edge and conical flank (FC-MBMT) made of cemented carbide is proposed, which reduces the difficulty of tool preparation through the design of the flat edge, and reduces the friction between the flank and the machined surface through the design of the conical flank. Firstly, based on the theory of the spherical helix, the mathematical model of FC-MBMT was established. Then, the motion expression of each axis of the machine tool in the grinding process of FC-MBMT is obtained by deriving the transformation matrix between the machine tool coordinate system and the tool coordinate system. The precision grinding of the FC-MBMT is realized, and its geometric parameter error is less than 8%. Finally, based on the above methods, two kinds of FC-MBMT with a flank width of 16 μm and a flank width of 24 μm were prepared, and their cutting performance was verified by micro groove milling experiments of martensitic steel. Ordinary equal guide cutting edge ball end milling tool participated in the machining as a comparison item. The milling experiment results show that the surface roughness of the FC-MBMT is less than 0.52 μm and the total cutting force is less than 7 N. The machining quality of the FC-MBMT with a conical flank width of 16 μm is better than the FC-MBMT with a flank width of 24 μm, and its cutting force is smaller than the FC-MBMT with a flank width of 24 μm, which indicates that it has better cutting performance with a conical flank width of 16 μm. The wear morphology shows that the wear forms of the FC-MBMT are chip adhesion on the conical flank and slight cutting edge wear. The anti-wear ability of the FC-MBMT with a conical flank width of 16 μm is obviously better than the FC-MBMT with a flank width of 24 μm. Compared with the ordinary micro ball end milling tool, the cutting performance and wear resistance of the FC-MBMT with a flank width of 16 μm are not significantly different. The experimental results verify the feasibility of the proposed tool structure.