Cognitive diagnostics in the Web-based Intelligent Education System (WIES) aims to assess students' mastery of knowledge concepts from heterogeneous, noisy interactions. Recent work has tried to utilize Large Language Models (LLMs) for cognitive diagnosis, yet LLMs struggle with structured data and are prone to noise-induced misjudgments. Specially, WIES's open environment continuously attracts new students and produces vast amounts of response logs, exacerbating the data imbalance and noise issues inherent in traditional educational systems. To address these challenges, we propose DLLM, a Diffusion-based LLM framework for noise-robust cognitive diagnosis. DLLM first constructs independent subgraphs based on response correctness, then applies relation augmentation alignment module to mitigate data imbalance. The two subgraph representations are then fused and aligned with LLM-derived, semantically augmented representations. Importantly, before each alignment step, DLLM employs a two-stage denoising diffusion module to eliminate intrinsic noise while assisting structural representation alignment. Specifically, unconditional denoising diffusion first removes erroneous information, followed by conditional denoising diffusion based on graph-guided to eliminate misleading information. Finally, the noise-robust representation that integrates semantic knowledge and structural information is fed into existing cognitive diagnosis models for prediction. Experimental results on three publicly available web-based educational platform datasets demonstrate that our DLLM achieves optimal predictive performance across varying noise levels, which demonstrates that DLLM achieves noise robustness while effectively leveraging semantic knowledge from LLM.