A variable altitude cooperative control method for a double-VGT two-stage adjustable supercharging system and a fuel common rail system of a diesel engine comprises the steps of 1 using a diesel engine variable-altitude multi-target and multi-parameter optimization algorithm to determine a diesel engine variable-altitude performance optimization target and the control parameters; 2, establishing aBP neural network ANN prediction model; (3) combining a particle swarm PSO multi-objective optimization algorithm with a neural network ANN for joint optimization, and taking an ANN model predictionvalue as an optimization sample; 2, using a cooperative control method of the double-VGT two-stage adjustable pressurization system and a fuel common rail injection system to cooperatively control theoil injection parameters, and improving the oil-gas-chamber matching of the diesel engine under a plateau condition. According to the method, based on the altitude and diesel engine working conditionchanges, the supercharging system controller and the oil injection system controller dynamically and cooperatively control the oil injection quantity, the oil injection advance angle, the HVGT and the LVGT of the diesel engine based on the MAP optimally calibrated by all the control parameters, so that the optimization and improvement of the dynamic property, the economical efficiency and the emission characteristic of the diesel engine within the altitude range of 0-5500 m are achieved.