Abstract The single event effects (SEEs) evaluations caused by atmospheric neutrons were conducted on three different convolutional neural network (CNN) models (Yolov3, MNIST, and ResNet50) in the atmospheric neutron irradiation spectrometer (ANIS) at the China Spallation Neutron Source (CSNS). The Yolov3 and MNIST models were implemented on the XILINX 28 nm system-on-chip (SoC). Meanwhile, the Yolov3 and ResNet50 models were deployed on the XILINX 16 nm FinFET UltraScale+ MPSoC. The atmospheric neutron SEEs on the tested CNN systems were comprehensively evaluated from six aspects, including chip type, network architecture, deployment methods, inference time, datasets, and the position of the anchor boxes. The various types of SEE soft errors, SEE cross-sections, and their distribution were analyzed to explore the radiation sensitivities and rules of 28 nm and 16 nm SoC. The current research can provide the technology support of radiation-resistant design of CNN system for developing and applying high-reliability, long-lifespan domestic artificial intelligence chips.