The growing need to provide secure communication in lightweight but resource-constrained systems like Internet of Things (IoT) and embedded systems, requires the development of lightweight and yet powerful cryptographic primitives. This paper introduces a lightweight block ciphering system using combinatorial substitution structures (CSS) that uses discrete combinatorial mappings to build the very nonlinear substitution layers. The proposed model combines algebraic transformations with permutation-based diffusion to attain high confusion and diffusion properties, with low computational complexity. An elaborate mathematical model is created to examine the algebraic complexity and algebraic and statistical attack resistance. The cipher architecture uses optimally constructed S-boxes based on the principles of combinatorics, which increases resistance to the differential and linear cryptanalysis. Through experimental analysis, the proposed approach is shown to increase security performance and efficiency over the traditional lightweight ciphers, which makes it an appropriate solution to the limited computing resources.