Abstract: Isochronous cyclotrons hold an indispensable position in national security and the science and technology innovation system. In the new era, there is an urgent demand for breakthroughs in compact structure, high energy, and high beam intensity of isochronous accelerators in major aerospace projects, frontier scientific research, and the medical and healthcare. Since 2000, China Institute of Atomic Energy (CIAE) has addressed the globally recognized fundamental technical challenge of insufficient focusing strength in isochronous accelerators. Through innovations in principle, engineering breakthroughs, and the systematic development of compact cyclotrons, CIAE has promoted the application of these accelerators in key fields, leading the development direction of compact high-intensity and superconducting cyclotrons both domestically and internationally. A total of nine cyclotrons of various models and energy levels—covering both high-intensity and superconducting types—have been designed and built, forming a relatively complete R&D system. CIAE has thus become an internationally influential center for isochronous accelerator research, focusing on pioneering research in three main directions: ultra-compact, ultra-lightweight, and high-power isochronous cyclotrons based on LTS and HTS technology.