Introduction: Balance impairment is an important indicator to a variety of diseases. Early detection of balance impairment enables doctors to provide timely treatments to patients, thus reduce their fall risk and prevent related disease progression. Currently, balance abilities are usually assessed by balance scales, which depend heavily on the subjective judgement of assessors. Methods: To address this issue, we specifically designed a method combining 3D skeleton data and deep convolutional neural network (DCNN) for automated balance abilities assessment during walking. A 3D skeleton dataset with three standardized balance ability levels were collected and used to establish the proposed method. To obtain better performance, different skeleton-node selections and different DCNN hyperparameters setting were compared. Leave-one-subject-out-cross-validation was used in training and validation of the networks. Results and Discussion: Results showed that the proposed deep learning method was able to achieve 93.33% accuracy, 94.44% precision and 94.46% F1 score, which outperformed four other commonly used machine learning methods and CNN-based methods. We also found that data from body trunk and lower limbs are the most important while data from upper limbs may reduce model accuracy. To further validate the performance of the proposed method, we migrated and applied a state-of-the-art posture classification method to the walking balance ability assessment task. Results showed that the proposed DCNN model improved the accuracy of walking balance ability assessment. Layer-wise Relevance Propagation (LRP) was used to interpret the output of the proposed DCNN model. Our results suggest that DCNN classifier is a fast and accurate method for balance assessment during walking.