Students' scientific thinking skills can be empowered by implementing certain learning models in which they are given opportunities to perform some scientific activities. This study aims at investigating: (1) effect of guided inquiry learning model on scientific thinking skills; (2) effect of different types of scientific activities on scientific thinking skills; and (3) interaction between learning model and type of scientific activities on scientific thinking skills. Design of this research is using Pre-Post test non equivalent group. The tests were based on Kuhn's scientific thinking skill indicators. There were 263 eleventh-grade science students in Pacitan, Indonesia, chosen as participants. Purposive sampling technique was used to determine its samples. The data were analysed by using ANCOVA (p = 0.05%) and LSD. The results of the study show that: (1) The guided inquiry had a highest potential to improve the students' scientific thinking skills; (2) The students with 'Type a' had a highest scientific thinking skill; (3) when the guided inquiry was implemented to the students with 'Type a', it gave a significant improvement to their scientific thinking skills. Based on this result, we should concern that the successful implementation of the guided inquiry is closely related to the students' scientific activity type.