Abstract: Magnet design and modeling is a crucial task in the design of cyclotrons, which includes iterative processes from an initial model. The magnetic field distribution should fulfill the requirements of isochronisms and transverse focusing of the beam, as well as avoiding dangerous resonance crossing. This paper introduces an automated magnet design, modeling and shimming method under the pythonic integrated environment based on virtual prototyping, a novel technique to shorten development period and reduce costs for physical prototypes. Detailed magnet shimming processes with the support of the 3D magnetic field simulation code TOSCA and an original developed particle tracking code PTP are described. As a case study, the main magnet design of a 16 MeV H- compact isochronous cyclotron is illus