SummaryUnderwater wireless sensor networks (UWSNs) based on autonomous underwater vehicles (AUVs) have become the standard technology for underwater search tasks with the advent of new underwater information and communication technologies (ICTs). It is also vulnerable to threats and malicious attacks because of its inherent characteristics, open acoustic channel and hostile underwater environment. The purpose of this research is to develop a secure data transfer (SDF) system based on software‐defined networking (SDN) architecture with cooperative searching scheme (CSS) (SDN‐SDF‐CSS) for AUV‐based UWSN. This part employs data, local control and the primary control layer to provide a scalable SDN‐based architecture for the AUV‐based UWSN. To accomplish the underwater search operation, the data layer is primarily deployed to gather AUVs (G‐AUVs) and store AUVs (S‐AUVs). In order to schedule the AUV, the clustering process takes place based on priority ranking with respect to the average power of each cluster. Then, the CSS is developed, and it is performed in the data layer. The hierarchical localization framework (HLF) can be used to locate each AUV's location within the data layer, which is a necessary step in deploying the cooperative searching model. Finally, for an efficient data transfer, the communication model is deployed in the data layer. UWSNs are vulnerable to various malicious attacks (such as bad‐mouthing attacks, on–off attacks, blackhole attacks and wormhole attacks) because of the high bit error rate and unstable optical/acoustic channels in the underwater environment. To overcome this, an SDF technique is used, which involves isolating the attacker node from the data layer. The suggested SDN‐SDF‐CSS model is implemented on the MATLAB platform, and its performance is evaluated using various evaluation metrics, both with and without attacks. As a result, the proposed SDN‐SDF‐CSS model has achieved better performance and proved its superiority in the UWSN environment.