The hydraulic shock absorber of a certain tractor suspension system is analyzed to determine the influence of the cross-sectional area ratio of the throttling holes of the restoration valve and the compression valve on the vibration damping performance of the whole vehicle, using a new method of machine-hydraulic co-simulation. First, the AMESim model of the hydraulic shock absorber is established, and the Kriging model is used to approximate the parameters of the AMESim hydraulic shock absorber model; the multi-island genetic algorithm and the gradient descent algorithm are used to obtain the three scenarios in which the cross-sectional area ratios of the throttle orifices of the same equivalent damping coefficients are greater than, equal to, or less than one. Then, a co-simulation model of 1/4 vehicle Recurdyn/AMESim and a co-simulation model of the whole vehicle with 162 degrees of freedom were established. The result show that, compared with the traditional method, this machine-hydraulic co-simulation method improves the calculation accuracy, calculation speed, and co-simulation model parameter accuracy. For low-speed conditions, when the throttle orifice area ratio equals 0.32, the minimum vehicle body center acceleration (root mean square value equal to 1.78 m/s2) is achieved. For high-speed driving conditions, when the throttle orifice area ratio is approximately 3.1, the minimum vehicle body center acceleration (root mean square value equal to 3.52 m/s2) is achieved.