Research on deep integration in publishing remains underdeveloped at the methodological level. Methodological awareness remains largely confined to borrowing tools from neighboring disciplines. Research methods have not fully addressed the distinctive nature of publishing integration, and clear disciplinary methodological awareness has not yet taken shape. Existing studies tend to equate integration methods with adding technology or moving content across platforms. The historical and relational character of publishing integration has not been fully discussed. After looking back at the origin and the conceptual shift in deep publishing integration, this paper begins with the Marxist view of publishing and proposes a philosophical framework for methodology organized around "consciousness, practice, and experience." In this framework, "consciousness" means researchers' reflection on the premises of publishing integration methods. "Practice" means specific publishing integration activities. "Experience" means the knowledge that emerges from practice and can be used again in method design. The framework treats the transformation of practice into experience as a focus of methodological reflection. It identifies unexamined premises in existing integration methods and addresses biases in methodological awareness. In this way, it provides a methodological foundation for the study of deep publishing integration. At the meso level, the paper centers on the interaction between "contextualism" and "holism." Contextualism focuses on the historical conditions and relational networks in which publishing integration takes place. By using interpretive and positivist methods, it analyzes historical events to examine how media, subjects, industries, and other elements connect and what forces drive them during the process of deep publishing integration from early growth, through practice, to rapid expansion. It also explains how these mechanisms form and operate in different historical contexts. This provides a "thick description" of the empirical context for understanding deep publishing integration. Holism focuses on system structure and the coordination of elements. It uses interpretive analysis, value network analysis, and agile development methods to examine the organizational structure and internal mechanisms of the deep publishing integration system. It redefines the boundaries of the system and its subsystems and introduces new elements such as technology and data in a systematic way. As a result, different elements within the system can work together and promote the overall evolution of the publishing ecology. At the macro level, the paper uses "dialectics, computation, and development" as coordinated dimensions. These three dimensions correspond to critical reflection, quantitative measurement, and historical change. With the help of collaborative computing, it measures the depth, breadth, and effectiveness of integration among people, machines, objects, and environments in the entire publishing value chain. Based on these measurements, it adjusts publishing integration models. Publishing integration practice is also placed within the strategic framework of overall social development. Through participatory and inclusive technology and publishing integration paths, it supports knowledge exchange and social and cultural development. The methodological framework built in this paper is still at the theoretical level. The next step is to test the explanatory power of contextualism and holism in concrete publishing integration cases and to improve the measurement indicators of collaborative computing.