The invention provides a permanent magnetic submersible linear motor and a manufacturing method thereof. The permanent magnetic submersible linear motor comprises a mover, a stator and a casing which are sequentially arranged from inside to outside, and resin filling materials are embedded into a gap between the stator and the mover and a gap between the stator and the casing. According to the permanent magnetic submersible linear motor, the gap between the stator and the mover and the gap between the stator and the casing are embedded through the resin filling materials, fully mixing and stirring the filling materials and then embedding the filling materials into the motor stator with an embedding tire are only required in an embedding process, welding during connecting a stainless steel cylinder with a stator core can be avoided, improving safety and quality reliability of the motor is facilitated, moreover, the embedded materials after curing exist in a solid mode, so the motor needs no quite high sealingness, processing precision and dimension requirements of each part of the motor are relatively loose, dimension in the embedding process depends on the embedding tire, and precision is higher compared with the stainless steel cylinder.