AbstractIn this paper, we obtain some basic results of quaternion algorithms and quaternion calculus on time scales. Based on this, a Liouville formula and some related properties are derived for quaternion dynamic equations on time scales through conjugate transposed matrix algorithms. Moreover, we introduce the quaternion matrix exponential function by homogeneous quaternion matrix dynamic equations. Also a corresponding existence and uniqueness theorem is proved. In addition, the commutativity of quaternion‐matrix–valued functions is investigated and some sufficient and necessary conditions of commutativity and noncommutativity are established on time scales. Also the fundamental solution matrices of some basic quaternion matrix dynamic equations are obtained. Examples are provided to illustrate the results, which are completely new on hybrid domains particularly when the time scales are the quantum case and the discrete case ; , both of which are significant for the study of quaternion q‐dynamic equations and quaternion difference dynamic equations. Finally, we present several applications including multidimensional rotations and transformations of the submarine, the gyroscope, and the planet whose dynamical behaviors are depicted by quaternion dynamics on time scales and the corresponding iteration numerical solution for homogeneous quaternion dynamic equations are provided on various time scales.