Exploring students' systems thinking (ST) is essential in enhancing science learning, but existing studies have failed to understand students' ST fully as it relates to ecological issues. This study aimed to fill the aforementioned literature gap by exploring lower-secondary school students' ST regarding ecological issues. The Systems Thinking Test regarding Ecological Issues, which measures four ST skills (system organisation, behaviour, application, and evaluation), was administered to 1,092 lower-secondary school students. The results reveal low ST performance in ecological issues, with students finding it particularly difficult to identify interactions among components and understand system characteristics. Furthermore, most lacked reflective consciousness and consideration of the diverse dimensions of ecological issues, resulting in monocausal reasoning in system decision-making and evaluation. Comparatively, urban school students performed better than their rural counterparts; additionally, an item-level analysis revealed that climate warming was challenging for the students to understand. This study suggests that greater efforts should be made to address students' drawbacks and that multi-perspectival teaching is necessary in the context of ecological issues. The addition of system decision-making and evaluation in assessments can enable a broader understanding of ST.