In science classrooms, technology affordance varies depending on device-student ratios (DSR) and the ways virtual manipulatives on mobile devices are used. Additionally, external scripts (ES) are widely used to promote effective group interaction in collaborative learning. Therefore, this research explored the influence of DSR and ES on collaborative inquiry learning. This research adopted a counterbalanced design between two rounds of experiments. A total of 128 students (including 11 dropouts) from four sixth-grade classes participated, with the four classes randomly divided into four experimental groups. Thematic analysis, social network analysis, and statistical analysis methods were used to analyze the distribution and transition of roles, the interaction between roles, and the self-efficacy and collective efficacy of the roles. The results illustrated that the role distribution was affected by DSR and ES, and frequent transitions of operational roles in groups emerged when DSR was exchanged. Moreover, the role of ES was reported in this study; it promoted the stability of role interaction on the one hand while significantly promoting self-efficacy and collective efficacy on the other. The study also proposed that the discourse statuses of different roles in collaborative learning were significantly different, and roles with a weaker discourse status had lower self-efficacy.