An intelligent tutoring system plays vital role in education and its importance is constantly increasing, meanwhile the key challenge in the teaching learning process is assessing students’ learning efficiently. In this paper, a hybrid assessment based-on ACT-R cognitive learning theory, combining ontology knowledge map with skills is proposed. In order to assess how well students master knowledge structure, an ontology knowledge map is constructed to describe declarative knowledge; and in order to assess how well students master knowledge skills, a problem solving process is constructed to describe procedural knowledge based on ACT-R. Finally, a student’s mastery of knowledge is assessed through both the knowledge map and skills in the problem solving process, as well as auxiliary indicators like time usage, prior knowledge level, self-assessment, etc. This method is implemented in a geometric intelligent assessment system and is evaluated in a junior high school. Experiments show that the assessment results are consistent with students’ actual learning levels. The hybrid cognitive assessment method can not only obtain the score of students’ mastery of knowledge points and the structure through knowledge map, but also assess the learning skills in problem solving process through exercises quantitatively.