Trusted data space (TDS) is a data circulation and utilization infrastructure that connects multiple stakeholders and realizes shared use of data resources based on consensus rules. As an application ecology for value co-creation of data elements, it serves as an important carrier to support the construction of a national integrated data market. Against this background, the compliant, correct and effective application of commercial cryptography to build a security foundation for TDS and realize the full life-cycle protection of data has become an urgent issue for the development of TDS and the compliant and efficient circulation of data elements. In view of the distributed federation architecture of trusted data space composed of a central service platform and multiple distributed access nodes, as well as its core functions of "centralized control, distributed execution, data in-domain, and available but invisible", this paper decouples the core architecture of TDS and divides it into five security domains. It systematically analyzes the typical security risks, and sorts out the cryptography application requirements and evaluation demands in full scenarios. On this basis, in strict accordance with the framework of GB/T 39786—2021, an indicator system and evaluation model for the security evaluation of commercial cryptography application adapted to TDS are constructed, and the effectiveness and applicability of the system are verified through theoretical analysis. This research provides references for the application and evaluation implementation of commercial cryptography.