Multimodal Large Language Models (MLLMs) have played an increasingly important role in multimodal intelligence. However, the existing fine-tuning methods often ignore cross-modal heterogeneity, limiting their full potential. In this work, we propose a novel fine-tuning strategy by injecting beneficial random noise, which outperforms previous methods and even surpasses full fine-tuning, with minimal additional parameters. The proposed Multimodal Noise Generator (MuNG) enables efficient modality fine-tuning by injecting customized noise into the frozen MLLMs. Specifically, we reformulate the reasoning process of MLLMs from a variational inference perspective, upon which we design a multimodal noise generator that dynamically analyzes cross-modal relationships in image-text pairs to generate task-adaptive beneficial noise. Injecting this type of noise into the MLLMs effectively suppresses irrelevant semantic components, leading to significantly improved cross-modal representation alignment and enhanced performance on downstream tasks. Experiments on two mainstream MLLMs, QwenVL and LLaVA, demonstrate that our method surpasses full-parameter fine-tuning and other existing fine-tuning approaches, while requiring adjustments to only about $1\sim2\%$ additional parameters. The relevant code is uploaded in the supplementary.