The “Institution Lag” between the demand for cross-border data services and the supply of rules constrains the in-depth development of cross-border data flow. The Guangdong Hong Kong Macao Greater Bay Area, as a strategic region with the highest degree of openness, the most significant institutional differences, and full of vitality and international competitiveness in China, has a particularly prominent internal tension between the autonomy demand for cross-border data flow and institutional standardization. This study takes the offshore data center of the Hetao Shenzhen-Hong Kong Science and Technology Innovation Cooperation Zone as an example, and combines the theory of ecological niche construction and organizational configuration to propose an analytical framework of “cross-border organizational configuration based on ecological niche construction”. It analyzes the conditional constraints of cross-border data flow in the Guangdong Hong Kong Macao Greater Bay Area and the establishment process of offshore data centers, explores the organizational configuration and institutional innovation mode of the data cross-border service system, and proposes to optimize the ecological niche construction of data cross-border services from the aspects of dislocation development, replenishment development, borrowing development, and expansion and expansion, in order to seek the best balance point between cross-border data flow security and freedom, promote the marketization and globalization of data elements.