The invention discloses a bilateral permanent magnet staggered type modular continuous pole permanent magnet synchronous linear motor. Bilateral permanent magnets are arranged in a staggered manner, the end force waveform and fluctuation rule of a continuous pole motor are adjusted, and a positioning force period is adjusted to take an electrical angle of 180 degrees as a period due to the arrangement manner that the permanent magnets are arranged in a staggered manner; meanwhile, positioning force harmonic waves generated by the end effect are basically eliminated, and the positioning force generated on the unit motor is counteracted due to reverse phases due to the arrangement of the length of the magnetic isolation structure, so the thrust fluctuation of the continuous pole motor is inhibited. By adjusting the phase sequence of the three-phase windings among the unit motors, on one hand, the electrical angles of the same-phase windings on different unit motors are basically the same, so that the average value of output thrust is not influenced; on the other hand, the magnetic field distribution of the end parts of the unit motors is adjusted, so that the relative positions of each phase winding on each unit motor and the end parts are different, the influence of the end part effect on the asymmetry of the three-phase windings is adjusted, the thrust fluctuation is finally inhibited, and the performance of a control system is improved.