Based on Bloom's Taxonomy of Educational Objectives and the assessment framework of PISA, this study aimed to develop a three-dimensional assessment framework to measure junior high school students' higher order thinking skills in mathematics in China. A total of 28,153 eighth graders from 11 districts and counties in Z city were involved in the test. The results showed that (1) in the "Mathematical ability" dimension, students scored the lowest in "Problem-solving"; (2) in the "Cognitive level" dimension, students scored the lowest in "Evaluate"; (3) there was little difference between students' scores on problems in "Realistic" and "Intramathematical situations"; (4) there were significant differences in the higher order thinking skills of students at different academic levels; and (5) there were no gender differences in students' higher order mathematical thinking skills (HOMTS). Implications for assessment in HOMTS and suggestions for future study are discussed.