This paper presents a novel approach to substantially improve the detection accuracy of structural damage via a one-dimensional convolutional neural network (1-D CNN) and a decision-level fusion strategy. As structural damage usually induces changes in the dynamic responses of a structure, a CNN can effectively extract structural damage information from the vibration signals and classify them into the corresponding damage categories. However, it is difficult to build a large-scale sensor system in practical engineering; the collected vibration signals are usually non-synchronous and contain incomplete structure information, resulting in some evident errors in the decision stage of the CNN. In this study, the acceleration signals of multiple acquisition points were obtained, and the signals of each acquisition point were used to train a 1-D CNN, and their performances were evaluated by using the corresponding testing samples. Subsequently, the prediction results of all CNNs were fused (decision-level fusion) to obtain the integrated detection results. This method was validated using both numerical and experimental models and compared with a control experiment (data-level fusion) in which all the acceleration signals were used to train a CNN. The results confirmed that: by fusing the prediction results of multiple CNN models, the detection accuracy was significantly improved; for the numerical and experimental models, the detection accuracy was 10% and 16–30%, respectively, higher than that of the control experiment. It was demonstrated that: training a CNN using the acceleration signals of each acquisition point and making its own decision (the CNN output) and then fusing these decisions could effectively improve the accuracy of damage detection of the CNN.