Despite the growing adoption of large language models (LLMs) in academic workflows, their capabilities remain limited in supporting high-quality scientific writing. Most existing systems are designed for general-purpose scientific text generation and fail to meet the sophisticated demands of research communication beyond surface-level polishing, for example, maintaining conceptual coherence across sections. Furthermore, academic writing is inherently iterative and revision-driven, a process that is not well supported by direct prompting-based paradigms. To address these scenarios, we propose a human-AI collaboration framework for academic paper revision, centered on criteria-guided intent alignment and context-aware modeling. To validate the framework, we curate a dataset of 7,000 research papers from top-tier venues, annotated with 140,000 instruction--response pairs that reflect realistic, section-level scientific revisions. We instantiate the framework in XtraGPT, the first suite of open-source LLMs (1.5B to 14B parameters) specifically fine-tuned for context-aware academic paper revision. Extensive experiments show that XtraGPT significantly outperforms same-scale baselines and rivals the quality of proprietary counterparts. Both automated preference assessments and human evaluations confirm the effectiveness of XtraGPT in improving scientific drafts. Our code and models are available at https://github.com/Xtra-Computing/XtraGPT and https://huggingface.co/collections/Xtra-Computing/xtragpt.