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Abstract Background Virtual simulation experiment is a vital component of higher education digitalization, emerging from the deep integration of specialty disciplines and information technology. Chinese universities have invested heavily in the construction of virtual simulation experiment projects, and the number of projects is considerably large. However, the popularity and effectiveness of these projects are not satisfactory. As an important index to measure the teaching quality, analyzing the influencing factors and mediating effects of learning satisfaction of virtual simulation experiment is an effective entry point to improve the quality and efficiency of virtual simulation experiment teaching and improve the learning effect. Methods This study used quantitative research methods. The research sample includes 538 students from various levels of higher education institutions such as Nanjing University, Nantong University, Nanjing Medical University, and Jiangsu University, covering 11 majors. They started to study the virtual simulation experiment course for one academic year in September 2023 and conducted a questionnaire survey at the end of the course. The questionnaire survey involved four aspects, mainly from the student dimension, course dimension, the technical dimension, and the embodied dimension to evaluate the learning satisfaction of the virtual simulation experiment course. The data were analyzed using SPSS and AMOS. Results According to the results of the structural equation modeling (SEM), all of the student dimension (learning motivation {β = 0.658,p |