A real-time intelligent route planning method is proposed in this paper for the geomagnetic navigation. Borrow ideas from classical particle swarm optimisation (PSO) algorithm, a two-subpopulation particle swarm optimisation (TSPSO) algorithm is given, which can track the changeable environment factor quickly and accurately. Based on TSPSO algorithm, a real-time route planning algorithm is researched including its two key points: route node extension and fitness function calculation. Simulation experiment results indicate that the real-time route planning method designed in this paper can track the changeable environment factor intelligently and replan a new route in time.