In this paper, we study the optimal control problem for a class of four-dimensional linear systems based on quaternionic and Fourier analysis. When the control is unconstrained, the optimal ensemble controller for this linear ensemble control systems is given in terms of prolate spheroidal wave functions. For the constrained convex optimisation problem of such systems, the quadratic programming is presented to obtain the optimal control laws. Simulations are given to verity the effectiveness of the proposed theory.