The Internet of Things (IoT) is a broad range of applications enabled by the connection of devices such as sensors, actuators, and monitors accessible through the Internet. Massive IoT device connectivity and vast data transmission have made the information susceptible to various types of attacks. Therefore, encryption is required for secure communication in an IoT ecosystem. An IoT system is constrained by its complexities that require small computing power. Thus, lightweight block cipher is chosen as the solution to IoT security issues. RECTANGLE block cipher has very efficient encryption speed performance among the existing lightweight algorithms. Although RECTANGLE achieves such high efficiency, lack of focus on its security aspect needs to be addressed. The algorithm is short of confusion and diffusion characteristics that should be offered by a block cipher as one of the cryptographic security properties. Therefore, we extended RECTANGLE using a 3D cipher to improve its security features by enhancing the algorithm confusion and diffusion properties. Security analysis and performance tests were performed to verify the strength of the proposed 3D RECTANGLE. The results show that 3D RECTANGLE performs better than its original version in terms of the correlation between data input and output with an increase of 1.58% for non-linearity results, records approximately 50% bit error rate for sensitiveness against both modifications of plaintext and key, increase of passing rate in the randomness test by 22.22%, and achieves competitive performance results against existing algorithms with 0.9516 ms execution speed and 67.26 bit/ms throughput.