The purpose of the research is to develop and identify the validity of factors affecting higher order thinking skills (HOTS) of students. The thinking skills can be divided into three types: analytical, critical, and creative thinking. This analysis is done by applying the meta-analytic structural equation modeling (MASEM) based on a database of 166 primary empirical studies. The research results assert the theories and bring conceptual and empirical clarity to the factors affecting HOTS of students and also give readers an understanding of the magnitude and significance of relationships among the variables in the model. MASEM results confirm that classroom environment, psychological and intellectual characteristics of students have direct effects on HOTS (96.8% explained variance). Whereas, the family characteristic had insignificant effects on HOTS but they had indirect effects on HOTS through psychological characteristic. Furthermore, we show that the most direct effects on HOTS were psychological characteristic, classroom environment and intellectual characteristic, respectively. This study provided a holistic view on the relationship of factors affecting HOTS and proposed a direction for future research and practice.