Aim and background: Today, students are encouraged to develop spatial visualization ability to meet the challenges of digital technologies impacting their daily life and education when exposed more time to a virtual 3D environment. This study investigated the effect of cognitive flexibility levels on students' spatial visualization abilities and computational thinking skills in three-dimensional design and coding training. In addition, this study examined the effect of the training on the spatial visualization abilities and computational thinking skills of the students. Method: The study employed a one-group pre-test/post-test quasi-experimental design. A total of 60 university students (51 female and 9 male) participated in this study. University students received three-dimensional design and coding training by using Tinkercad. The Spatial Visualization Test, the Cognitive Flexibility Scale, the Computational Thinking Scale and semi-structured interview form were used to collect data. Paired samples t-test and one-way ANCOVA were used for the data analysis. Results and discussion: Results from the training indicated that the students' spatial visualization abilities improved. Their spatial visualization abilities and computational thinking skills were related to their cognitive flexibility levels. The training also improved the spatial visualization abilities and computational thinking skills of students with high cognitive flexibility. 3D design and coding education could be more effective for students with high cognitive flexibility. The qualitative findings supported the results of the study.