Diffusiophoresis is a common phenomenon that occurs when colloids are placed in the non-uniform solute concentration. It generates solute gradients which force the colloids to transfer toward or away from the higher solute concentration side. In this paper, we consider the input sequence control of the colloid transport in a dead-end micro-channel with a boundary solute concentration being manipulated, which has a wide range of applications such as drug delivery, biology transport, oil recovery system and so on. We model this process by a coupled system, which involves the solute diffusion equation and the colloid transport model. Then an optimal control problem is formulated, in which the goal is to minimize colloid density distribution deviation between the computational one and the target at a pre-specified terminal time. To solve this partial differential equation (PDE) optimal control problem, we first apply the control parameterization method to discretize the boundary control and transfer it into an optimal parameter selection problem. Then, using the variational method, the gradient of the objective function with respect to the decision parameters can be derived, which depends on the solution of the coupled system and the costate system. Based on this, we propose an effective computational method and a gradient-based optimization algorithm to solve the optimal control problem numerically. Finally, we give the simulation results to demonstrate that the objective function based on the proposed method is less nearly two orders of magnitude than that of a constant value control strategy, which well illustrates the effectiveness of the proposed method.