Integral to fostering computational thinking (CT) skills, which are increasingly essential in today's digital era, has been the shift of paper-based pictorial modeling activities to computational modeling. Research has indicated that modeling activities can advance students' understanding of a system's mechanism (i.e., systems thinking), such as an ecosystem. The current study examines the impacts of paper-based pictorial and computational modeling activities on students' systems thinking and CT skills. A total of 751 seventh-grade students were involved in online modeling activities, spanning over 4 days, and were assigned purposefully to a paper-based modeling condition (n = 374) or a computational modeling (n = 377) condition. They took systems-thinking-embedded food web and CT assessments before and after the four activities, in addition to a formative assessment after each activity. Multilevel modeling and repeated-measures correlation tests were used to analyze the students' quantitative data. Epistemic network analysis (ENA) was utilized to map out students' perceptions of what they believed they learned from the activities. The results revealed significant increases in the systems thinking-embedded food web constructs in both conditions. However, the increase of CT skills in the paper-based pictorial condition was not as significant as the increase in the computational modeling condition. ENA results showed that students in the computational modeling condition had more co-occurrences between science and computer science or CT concepts than those in the paper-based pictorial condition. These findings illuminate the benefit of engaging students in computationally rich science activities to advance both systems thinking and CT skills.