The invention provides a spacecraft guidance control method and system based on non-linear orbit calculation. The method includes the steps that firstly, a system state equation for current orbit calculation of a spacecraft is acquired, a low-order equation of control variables is acquired after dimension reduction, then the control variables are acquired by calculating intermediate quantities acquired after dimension reduction, finally, a flight orbit of the spacecraft is controlled according to the control variables, the change of parameters relevant to spacecraft orbit calculation is checked in a period designated by a user, if the change is checked, the control variables are recalculated, the flight orbit of the spacecraft is adjusted, and if no change is checked, the spacecraft runs according to the originally-calculated orbit. The gap in the field of traditional spacecrafts is filled in, the spacecraft has real-time optical orbit tracking capacity, and the expression of the spacecraft in the aspects of obstacle avoidance, interception breakthrough and the like is improved.