Controller Area Network with Flexible Data-rate (CAN FD) is beneficial for the in-vehicle communication of Internet of Connected Vehicles (IoCVs) because of its high bandwidth and data field length. However, CAN FD lacks a security authentication mechanism, making it extremely vulnerable to masquerade attacks. This study proposes the security enhancement for a real-time parallel in-vehicle application adopting a two-stage method. The first stage obtains the lower bound of an in-vehicle application by quickly abandoning most of sequences, while the second stage enhances security by adding Message Authentication Codes (MACs) to messages taking advantage of the laxity interval from the lower bound to the deadline. Experiments with an example and the adaptive cruise control in-vehicle application show the advantage of the proposed two-stage method in increasing the total byte size of MACs.