Scientific data has become both foundational materials and outcomes of scientific research with important value. However, among 2358 engineering science journals indexed in CNKI, only 64 journals have published scientific data on ScienceDB. To address the discrepancy between the publication of scientific data and that of academic papers in engineering science journals, a comprehensive analysis was conducted to investigate the characteristics of the aforementioned scientific data. This analysis led to the formulation of publishing principles for scientific data and the establishment of a scientific data publishing process integrated with the submission and peer review system. The scientific data associated with engineering science journal papers are characterized as the data that documents the state of scientific research objects, while cannot be fully presented in printed or digital journal formats. These data must be preserved, processed, and transmitted using digital means. An analysis of the evolving trends in engineering science research activities and outputs reveals a progressive shift in the role of scientific data relative to journal papers. Such data are increasingly recognized as a crucial supplementary material, characterized by broad scope, diverse formats, and the involvement of third parties in intellectual property protection. The current status of scientific data publishing in engineering science journals was presented, revealing that only 2.71% of these journals indexed in CNKI publish scientific data, with an average of 12.33 datasets published per issue. To foster scientific data sharing, a set of publishing principles that benefit data producers (authors), users (readers), and disseminators (journals) was proposed. First, authors retain control over what scientific data is shared, how it is shared, and when to share it. Second, scientific data is treated as a citable publications, and are disseminated for the benefit of the public. Finally, the maintenance of data confidentiality is imperative. The publication system of scientific data related to engineering science journal papers was designed, outlining the responsibilities and workflows across major stages, such as preliminary review, secondary review, final review, and external review. This system aligns the proposed publication principles with the three-tier peer review system currently used for the publication of papers. Furthermore, the scientific data publishing process was adapted to the submission and peer review system, and the workflow diagrams of scientific data publishing, correction, and updates were demonstrated. The items of formatting forms, for the scientific data detail sheet and the expert review sheet, were specified to improve the efficiency and standardization of scientific data publishing.