As low-carbon and sustainable manufacturing becomes the mainstream development direction of the current manufacturing industry, the traditional heavy industry manufacturing enterprises in China urgently need to transform. For the heavy cement equipment manufacturing enterprise investigated here, there is a large amount of energy waste during the manufacturing operation due to scheduling confusion. In particular, the multispeed, multi-function machining and the transportation of multiple automated guided vehicles (multi-AGV) are the main influencing factors. Therefore, this paper addresses a novel low-carbon scheduling optimization problem that integrated multispeed flexible manufacturing and multi-AGV transportation (LCSP-MSFM & MAGVT). First, a mixed-integer programming (MIP) model is established to minimize the comprehensive energy consumption and makespan in this problem. In the MIP model, a time-node model is built to describe the completion time per workpiece, and a comprehensive energy consumption model based on the operation process of the machine and the AGV is established. Then, a distribution algorithm with a low-carbon scheduling heuristic strategy (EDA-LSHS) is estimated to solve the proposed MIP model. In EDA-LSHS, the EDA with a novel probability model is used as the main algorithm, and the LSHS is presented to guide the search direction of the EDA. Finally, the optimization effect and actual performance of the proposed method are verified in a case study. The experimental results show that the application of the proposed method in actual production can save an average of 43.52% comprehensive energy consumption and 64.43% makespan, which effectively expands the low-carbon manufacturing capacity of the investigated enterprise.