The Internet of Things (IoT) applications are considered as smart device applications because of its remote monitoring/ controlling access. The vast quantity of devices is linked with heterogeneous IoT infrastructures which increases various attacks in IoT applications. Therefore, the security analysis should be evaluated to find out the best secured encryption process before implementing IoT applications. Moreover, lightweight algorithms are suitable for small power and high speed IoT devices. In this paper, lightweight algorithm is chosen because of its faster speed among other algorithms. However, the security of lightweight algorithms is not satisfactory for IoT/mHealth applications. To enhance the security of lightweight algorithms, we have designed a 4x4 composite S-Box rather than Look Up Table (LUT) method. Additionally, the composite S-Box value is again secured using 3D cipher for confusion and diffusion process to improve its security. Thus, we have proposed a lightweight 3D Composite S-Box which will give more security compared to other existing S-Boxes.