Using many-facets Rasch measurement, this study aimed to detect and measure disciplinary context effects on student hands-on performance in terms of scientific inquiry competence. In Shanghai, China, a total of 251 eighth graders, from five junior high schools, participated in this study. The partial credit Rasch model was applied to help establish evidence of the validity and reliability of the hand-on based performance instrument measures. The findings indicate that there are significant disciplinary context effects on student performance in terms of scientific inquiry competence. Some inquiry competences embedded in one disciplinary context could be significantly more difficult (or easier) for participants than in other contexts. This study also reveals that there are significant differences in difficulty measures among inquiry competences. Implications and suggestions for science teaching and assessment are also discussed.