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University students face a rising prevalence of depression, anxiety, insomnia, and suicidal ideation that exceeds the capacity of conventional, resource-constrained campus support services. Although artificial intelligence (AI)-assisted screening tools have emerged, many have evaluated selected modalities or isolated prediction tasks, and their integration with prospectively evaluated intervention pathways remains limited. This protocol describes the Comprehensive Artificial Intelligence-Assisted Mental Health Program for University Students in China (CAMPUS), a multi-center research program comprising a five-year prospective cohort, eight planned embedded randomized controlled trials, and exploratory multimodal AI and multi-omics studies across seven Chinese universities. Longitudinal cohort enrolment commenced at Henan Medical University in September 2025 and is planned to expand across seven participating universities. Multidimensional screening integrates psychological self-report (PHQ-9, GAD-7, ISI, BSI-CV, and others), physiological measurements (EEG, MRI, fNIRS, HRV, eye tracking, facial-expression analysis, ERP, voice acoustics), and an exploratory biospecimen component for multi-omics profiling, potentially including genomic, transcriptomic, proteomic, metabolomic, and microbiome analyses, subject to the finalization and approval of layer-specific protocols. Students identified through cohort screening as potentially eligible for an intervention trial will undergo trial-specific eligibility assessment. Those who meet the eligibility criteria and provide trial-specific informed consent will be individually randomized in a 1:1 ratio to the intervention or its comparator within one of eight separate two-arm, multi-center, parallel-group randomized controlled trials. A Transformer-based multimodal AI framework with SHAP-based feature attribution will be developed and internally evaluated for questionnaire-defined risk stratification and exploratory treatment-response prediction. The initial Henan Medical University cohort recruitment and university-student mental-health assessment were approved by the Ethics Review Committee of Henan Medical University (XYLL-20250484), and written informed consent is obtained from participants before enrolment. Each additional participating center will obtain local ethics approval before study activation. Findings will be disseminated through peer-reviewed publications, scientific conferences, and policy briefs, providing evidence that may inform the design and prospective evaluation of youth mental-health programs in other university settings. The two clinical trials were registered in the Chinese Clinical Trial Registry (ChiCTR). The registration details and URLs are as follows: ChiCTR2500113527: https://www.chictr.org.cn/showproj.html?proj=298271 ; ChiCTR2500113613: https://www.chictr.org.cn/showproj.html?proj=298268 .