An ion trap system and an ion trapping method are provided. The ion trap system may include: an ion source, configured to: generate an ion, and shoot the ion to an ion trap; the electromagnetic field device, configured to change a moving direction of the ion, to transfer the ion to an ion trap; and the ion trap, configured to trap the ion transferred by the electromagnetic field device. The electromagnetic field device changes the moving direction of the ion, to transfer the ion to the ion trap.