Microbial Fuel Cells (MFCs) offer a promising pathway for sustainable energy generation by converting organic matter into electricity through microbial processes. A key factor influencing MFC performance is the anode structure, where design and material properties play a crucial role. Existing predictive models struggle to capture the complex geometric dependencies necessary to optimize these structures. To solve this problem, we propose KANGURA: Kolmogorov-Arnold Network-Based Geometry-Aware Learning with Unified Representation Attention. KANGURA introduces a new approach to three-dimensional (3D) machine learning modeling. It formulates prediction as a function decomposition problem, where Kolmogorov-Arnold Network (KAN)- based representation learning reconstructs geometric relationships without a conventional multi- layer perceptron (MLP). To refine spatial understanding, geometry-disentangled representation learning separates structural variations into interpretable components, while unified attention mechanisms dynamically enhance critical geometric regions. Experimental results demonstrate that KANGURA outperforms over 15 state-of-the-art (SOTA) models on the ModelNet40 benchmark dataset, achieving 92.7% accuracy, and excels in a real-world MFC anode structure problem with 97% accuracy. This establishes KANGURA as a robust framework for 3D geometric modeling, unlocking new possibilities for optimizing complex structures in advanced manufacturing and quality-driven engineering applications.