Characterizing materials with electron micrographs is a crucial task in fields such as semiconductors and quantum materials. The complex hierarchical structure of micrographs often poses challenges for traditional classification methods. In this study, we propose an innovative backbone architecture for analyzing electron micrographs. We create multi-modal representations of the micrographs by tok-enizing them into patch sequences and, additionally, representing them as vision graphs, commonly referred to as patch attributed graphs. We introduce the Hierarchical Network Fusion (HNF), a multi-layered network structure architecture that facilitates information exchange between the multi-modal representations and knowledge integration across different patch resolutions. Furthermore, we leverage large language models (LLMs) to generate detailed technical descriptions of nano-materials as auxiliary information to assist in the downstream task. We utilize a cross-modal attention mechanism for knowledge fusion across cross-domain representations(both image-based and linguistic insights) to predict the nanomaterial category. This multi-faceted approach promises a more comprehensive and accurate representation and classification of micrographs for nanomaterial identification. Our framework outperforms traditional methods, overcoming challenges posed by distributional shifts, and facilitating high-throughput screening.