We propose a security verification framework for cryptographic protocols using machine learning. In recent years, as cryptographic protocols have become more complex, research on automatic verification techniques has been focused on. The main technique is formal verification. However, the formal verification has two problems: it requires a large amount of computational time and does not guarantee decidability. We propose a method that allows security verification with computational time on the order of linear with respect to the size of the protocol using machine learning. In training machine learning models for security verification of cryptographic protocols, a sufficient amount of data, i.e., a set of protocol data with security labels, is difficult to collect from academic papers and other sources. To overcome this issue, we propose a way to create arbitrarily large datasets by automatically generating random protocols and assigning security labels to them using formal verification tools. Furthermore, to exploit structural features of protocols, we construct a neural network that processes a protocol along its series and tree structures. We evaluate the proposed method by applying it to verification of practical cryptographic protocols.