A magnetic field based time-of-flight mass spectrometer setting method of an ion well adopts an ion source generation module, an ion introduction and screening module, an ion well module, a flight disc module and a detector module. The method comprises the following steps of making an introduced sample ionized by the ion source module and then focused or screened by an ion focusing and screening module; entering the ion well module for enrichment; resetting an ion space position; introducing the sample into the flight disc module in an uniform Lorentz magnetic field; controlling ion flight circle; and finally, allowing an ion to reach a detector to complete signal detection. The flight disc module is used for setting the Lorentz magnetic field on a flight track, the flight of the ion is controlled to be a round track by the Lorentz magnetic field, the flight circle of the ion is controlled, and the time of iron reaching the detector is counted to carry out ion quantification.