Flexible job-shop scheduling problem (FJSP) is a new research hotspot in the field of production scheduling. To solve the multiobjective FJSP problem, the production of flexible job shop can run normally and quickly. This research takes into account various characteristics of FJSP problems, such as the need to ensure the continuity and stability of processing, the existence of multiple objectives in the whole process, and the constant complexity of changes. It starts with deep learning neural networks and genetic algorithms. Long short-term memory (LSTM) and convolutional neural networks (CNN) are combined in deep learning neural networks. The new improved algorithm is based on the combination of deep learning neural networks LSTM and CNN with genetic algorithm (GA), namely, CNN-LSTM-GA algorithm. Simulation results showed that the accuracy of the CNN-LSTM-GA algorithm was between 85.2% and 95.3% in the test set. In the verification set, the minimum accuracy of the CNN-LSTM-GA algorithm was 84.6%, both of which were higher than the maximum accuracy of the other two algorithms. In the FJSP simulation experiment, the AUC value of the CNN-LSTM-GA algorithm was 0.92. After 40 iterations, the F1 value of the CNN-LSTM-GA algorithm remained above 0.8, which was significantly higher than the other two algorithms. CNN-LSTM-GA is superior to the other two algorithms in terms of prediction accuracy and overall performance of FJSP. It is more suitable for solving the discrete manufacturing job scheduling problem with FJSP characteristics. This study significantly raises the utilisation rate of the assembly shop’s equipment, optimises the scheduling of FJSP, and fully utilises each processing device’s versatile characteristics, which are quite useful for the production processes of domestic vehicle manufacturing companies.