With the remarkable growth of the Internet and communication technologies over the past few decades, Internet of Things (IoTs) is enabling the ubiquitous connectivity of heterogeneous physical devices with software, sensors, and actuators. IoT networks are naturally two-layer with the cloud and cellular networks coexisting with the underlaid device-todevice (D2D) communications. The connectivity of IoTs plays an important role in information dissemination for missioncritical and civilian applications. However, IoT communication networks are vulnerable to cyber attacks including the denialof-service (DoS) and jamming attacks, resulting in link removals in IoT network. In this work, we develop a heterogeneous IoT network design framework in which a network designer can add links to provide additional communication paths between two nodes or secure links against attacks by investing resources. By anticipating the strategic cyber attacks, we characterize the optimal design of secure IoT network by first providing a lower bound on the number of links a secure network requires for a given budget of protected links, and then developing a method to construct networks that satisfy the heterogeneous network design specifications. Therefore, each layer of the designed heterogeneous IoT network is resistant to a predefined level of malicious attacks with minimum resources. Finally, we provide case studies on the Internet of Battlefield Things (IoBT) to corroborate and illustrate our obtained results. Fig. 1: In IoBT networks, a team of UAVs and a group of soldiers and UGVs execute missions cooperatively. The agents in the battlefield share critical information through D2D communications. The UAV network and ground network form a two-layer network which faces cyber threats, e.g., jamming attacks which can lead to link removals.network in a battlefield which can be susceptible to jamming attacks. It is essential to design communication networks that can allow the IoBT networks to be robust to natural failures and secure to cyber attacks in order to keep a high-level situational awareness of agents in a battlefield.Due to heterogeneous and multi-tier features of the IoT networks, the required security levels can vary for different networks. For example, in IoBT networks, the connectivity of UAV networks requires a higher security level than the ground network if the UAVs are more likely to be targeted by the adversary. Similarly, in vehicular networks, the communication links between RSUs need a high-level protection when they anticipate more attacks than the vehicles do. Therefore, it is imperative to design secure IoT networks resistant to link attacks and maintain the two-layer network connectivity with heterogeneous security requirements simultaneously. To this end, we present a heterogeneous IoT network design framework in which network links are vulnerable to malicious attacks. To enhance the security and the robustness of the network, an IoT network designer can add extra links to provide additional communication paths b...