Intrusion detection is considered the process of examining or monitoring traffic in the network, user behavior, and system function, to recognize the unofficial anomalous or access actions that could indicate the cyberattacks or security breaches. In intrusion detection, unifying multiple features causes redundancy, and irreverent features are added and causing a waste of computational resources. Thus, this research presented a new technique named Jensen Shannon Deep Kronecker Networks with Deep Stacked Autoencoders (JS-DKN +DSA) for feature fusion in IoT intrusion detection. At first, the simulation of IoT is performed, and thereafter, the input network traffic data is applied to data normalization. Furthermore, the z-score is utilized for data normalization to improve the quality of data. Thereafter, feature fusion is performed by the Jensen Shannon with Deep Kronecker Networks (JS-DKN), in which the JS is employed to find the relevant features, and the DKN is applied to find the fusion coefficient. Lastly, intrusion detection in IoT is effectuated by the Deep Stacked Autoencoder (DSA) and produces output as attack or normal. In addition, the presented JS-DKN +DSA approach recorded the highest accuracy of 90.876%, True Negative Rate (TNR) of 88.654%, and a True Positive Rate (TPR) of 92.766 %.