The latest emerging transdisciplinary marine protected area (MPA) research scheme requires efficient approaches for theoretically based and data-driven method integration. However, due to the rapid development and diversification of research methods, it is growingly difficult to locate new methods in methodological dimensions and integrate them to the utmost utility. This study proposes a deep learning-based classification framework for MPA management methods focused particularly on data and theory capabilities using natural language processing (NLP). It extracted keywords from academic sources and performed clustering based on semantic similarity, generating benchmark texts for abstract labeling. By training the deep learning NLP model and analyzing the abstracts of 9049 MPA management empirical research articles from 1986 to 2024, the data and theory scores were attributed to each article, and a total of 19 major method categories and 110 segment branches were identified in qualitative, quantitative, and mixed genres. Combination types of research methods were summarized, yielding the data-theory neutralization principle where the average data and theory scores tend to approximate 0.50. Applying the principle broadens traditional boundaries for method integration and extends method synthesis to higher numbers, generating a practical research 2paradigm for future MPA research. Implications include bridging social and ecological data, theorizing emergent challenges in complex systems and integrating theory construction and data science. The framework is applicable to quantification of other environmental management disciplines and can serve as guidance for multidisciplinary method integration.© 2017 Elsevier Inc. All rights reserved.