The installation of the Electronic Braking System (EBS) could effectively improve braking response speed, shorten braking distance, and ensure driving safety of commercial vehicles. However, during longitudinal deceleration control process, the commercial vehicles face not only challenges such as large inertia mass and random road gradient resistance of the vehicle layer, but also non-linear characteristics of the EBS actuator layer. In order to solve these problems, this paper proposes a commercial vehicle’s longitudinal deceleration precise control strategy considering vehicle-actuator dynamic characteristics. First, longitudinal dynamics of commercial vehicle is analyzed, and so is the EBS’ non-linear response hysteresis characteristics. Then, we design the dual layer deceleration control strategy. In vehicle layer, the recursive least squares with forgetting factor and Kalman filtering are comprehensively applied to dynamically estimate the vehicle mass and driving road slope. Based on the vehicle dynamics feedforward module, we have successfully converted target deceleration request of commercial vehicle into the EBS’ target braking pressure. At the same time, the Proportional-Integral-Derivative (PID) is used as feedback control to improving deceleration following accuracy. In the actuator layer, the EBS’ boosting, holding, and reducing pressure coordination control logic is designed. In order to achieve brake pressure following, we also utilize the fuzzy theory to establish the mapping relationship between the EBS’ non-linear response characteristics and the parameters of pressure closed-loop PID controller. Finally, a joint simulation platform is built based on MATLAB/Simulink, TruckSim, and AMESim. The simulation results demonstrate the designed deceleration control algorithm could help commercial vehicle achieve precise braking deceleration follow-up effects in various experimental conditions.