How to delete data in @ManyToMany relation in Nest.js

I think making your entities relations bidirectional should work:

@Entity()
export class Device{

  @PrimaryColumn()
  Name:string;    

  @Column({ nullable: true})
  Port:number;

  @Column({ nullable: true})
  IPadress:string;

  @Column({ nullable: true})
  Location:string;

  @ManyToMany(type => User, users => users.devices { cascade: true })
    @JoinTable()
    users: User[];

  }

@Entity()
export class User{

  @PrimaryColumn()
  Id:number;
  @Column({ nullable: true})
  Departement:string;
  @Column({ nullable: true})
  FirstName:string;
  @Column({ nullable: true})
  LastName:string;
  @Column({ nullable: true})
  CardNumber:string;
  @Column({ nullable: true})
  MobilePhone:string;
  @ManyToMany(type => Device, device => device.users)        
    devices: Device[];
}

I suppose you're already set your datasource, so you can remove only user by:

db.getRepository(User).delete(userId);

and when you delete one device, it will delete all his associated users:

db.getRepository(Device).delete(deviceId);