Computational thinking (CT) has received much attention in mathematics education in recent years, and researchers have begun to experiment with the integration of CT into mathematics education to promote students' CT and mathematical thinking (MT) development. However, there is a lack of empirical evidence and new theoretical perspectives on the mechanisms of interaction between CT and MT. To address this research gap, this study analyses the participants' thinking processes in solving programming-based mathematical problems from a flexibility perspective, focusing on the interplay between computational and mathematical thinking, that is, how CT and MT work together to influence and determine the problem-solver's choice of solution strategy. Using data collected from a large design-based study, we summarise two types of flexibility and six subtypes of flexibility demonstrated by participants in the programming-based mathematical problem-solving process using thematic analysis. These different types of flexibility provide researchers and mathematics educators with new theoretical perspectives to examine the interplay of CT and MT. Findings will also contribute toward student learning characteristics in programming-based mathematical problem-solving to sketch the big picture of how CT and MT emerge in complementary or mismatching ways.