In battery management systems, state of charge (SOC) estimation is important for ensuring the safety and reliability of batteries. Currently, there are various methods for estimating SOC, and the neural network method is the most popular. However, when the battery’s SOC is low (below 20%), the uncertainty in neural network parameters can lead to significant bias in SOC estimation. To address these problems, this study proposes a method based on genetic algorithm (GA) optimization of a time-serialization convolutional neural network (TSCNN) model. First, the population is initialized according to the optimized hyperparameters of the TSCNN model, whereby the experimental data are converted into time-series data. Subsequently, neural network models are built based on the population, thereby using the effect of the network as the fitness function for GA optimization. Finally, an optimized network structure is obtained for accurate SOC estimation. During the optimization process, the optimized data exhibited abnormal phenomena, usually manifested as exceeding the data limits or being zero. In the past, abnormal data were discarded and new data were regenerated; however, this reduces the correlation between data. Therefore, this study proposes a check function to enhance the correlation between the data, converting abnormal data into normal data by limiting the data range. To the best of our knowledge, it is the first time that a GA is being proposed to optimize the time-series length of a convolutional neural network (CNN) while the neural network parameters are optimized so that the time-series length and neural network parameters achieve the best match. In the experimental results, the maximum error was 4.55% for the dynamic stress test (DST) dataset and 2.58% for the urban dynamometer driving schedule (UDDS) dataset. When the battery SOC was below 20%, the estimation error did not incur a huge error. Therefore, the optimization method proposed for the TSCNN model in this study can effectively improve the accuracy and reliability of SOC estimation in the low-battery state.