Continuous-variable quantum key distribution (CV QKD) with discrete modulation has attracted increasing attention due to its experimental simplicity, lower-cost implementation and compatibility with classical optical communication. Correspondingly, some novel numerical methods have been proposed to analyze the security of these protocols against collective attacks, which promotes key rates over one hundred kilometers of fiber distance. However, numerical methods are limited by their calculation time and resource consumption, for which they cannot play more roles on mobile platforms in quantum networks. To improve this issue, a neural network model predicting key rates in nearly real time has been proposed previously. Here, we go further and show a neural network model combined with Bayesian optimization. This model automatically designs the best architecture of neural network computing key rates in real time. We demonstrate our model with two variants of CV QKD protocols with quaternary modulation. The results show high reliability with secure probability as high as $99.15\%-99.59\%$, considerable tightness and high efficiency with speedup of approximately $10^7$ in both cases. This inspiring model enables the real-time computation of unstructured quantum key distribution protocols' key rate more automatically and efficiently, which has met the growing needs of implementing QKD protocols on moving platforms.