Science classroom learning environment (CLE) and science teacher professional development (PD) are two important factors in students' science learning. However, the nature of the science CLE and school-level PD that promotes students' science achievement remains unclear. Using the Program for International Student Assessment (PISA) 2015 data, this study aims to explore the multi-level relationships between student-reported CLE, school-level teacher PD, and the possible interaction effects between the two on students' science achievement. Since sample students were nested within schools, two-level hierarchical linear models (HLM) were used to analyze the data. Results indicated that science CLE factors, including direct instruction, adaption of instruction, and disciplinary climate, had significantly positive relationships with students' science achievement, while inquiry-based science teaching and learning practices and perceived feedback had significantly negative relationships with students' science achievement. Moreover, these relationships varied significantly between schools. For school-level PD factors, the proportion of PD in school science and proportion of teachers attending PD within 12 months had significantly positive relationships with students' average science achievement between schools. More importantly, a significant cross-level interaction effect was found between PD requirements and disciplinary climate. Implications for creating science CLEs to promote students' science learning, including implementing science teacher PD through a school-level approach and modifying PD based on CLE contextual factors, are also provided.