This study investigated the impact of grouping methods on free inquiry implementation through the use of mixed research methods. Some 113 7th graders and 2 science teachers in two middle schools participated in this study. The 113 students who participated in this study were grouped by homogeneity and heterogeneity according to scientific inquiry skills and personality types respectively, and performed free inquiry activities on the same subject for three weeks. Data were collected by means of a test on science inquiry skills and from focus group interviews with 36 students and in-depth interviews with 2 teachers. The quantitative results of this study showed that homogeneous grouping was more effective than heterogeneous grouping in improvement of scientific inquiry skills. Meanwhile, the qualitative results revealed both the students and teachers perceived that it was effective to compose a small group according to their affective quality than their cognitive quality. Particularly, most of the students preferred the method of small group from the personality types. Some students and both teachers proposed that it is necessary to collect enough information on students and to use them in mixture with the method of small group according to the affective quality.