The construction of a standard system is a fundamental project for achieving the standardization of smart farms. In response to the key issues existing in the current construction of smart farms for cotton production, such as fragmented standard systems, low levels of standardization, and incomplete data sharing mechanisms, based on a systematic review of the current status and standardization needs of smart farms for cotton production, the core principles and paths for the construction of the standard system were established. Through integrating modified Checkland methodology and Hall’s three-dimensional structure model, a novel three-dimensional architecture encompassing hierarchical, procedural, and professional dimensions was proposed. The developed framework comprised five standardized clusters: fundamental and general standards, data standards, product standards, methodological standards, and management/service standards, achieving vertical integration across standard levels and horizontal coverage of operational processes. To validate system efficacy, a fuzzy analytic hierarchy process (FAHP) comprehensive evaluation model incorporating four primary and seven secondary indicators was established, with evaluation results demonstrating good applicability (grade Ⅱ) and significant implementation value. This research provided theoretical foundations for standard system development in China’s smart cotton production.