Modern learning focuses on active student engagement through thinking, creativity, and collaboration, supported by PjBL and AI to suit the digital era. This study explores the impact of AI-assisted project-based learning (PjBL) on students' analytical thinking, creative thinking, and collaboration skills in biology education, focusing on the circulatory system. Using a quasi-experimental design with 80 eleventh-grade students (40 experimental, 40 control) from SMAN 1 Magelang, Indonesia, the research employed MANOVA and ANOVA to analyze posttest scores. Results revealed significant improvements in the experimental group, with mean differences of 5.67 (analytical thinking, *p* = 0.001), 4.12 (creative thinking, *p* = 0.010), and 3.89 (collaboration, *p* = 0.015). AI tools enhanced analytical skills through data visualization and feedback, fostered creativity via simulations and iterative problem-solving, and supported collaboration via AI-driven task allocation and communication platforms. However, collaboration gains were more modest, underscoring the enduring role of interpersonal dynamics. The study concludes that integrating AI into PjBL effectively cultivates higher-order thinking skills, though its implementation requires balancing technological and human-centric pedagogical approaches. These findings advocate for AI as a transformative tool in biology education, provided ethical and accessibility considerations are addressed.
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