The advent of cloud computing as a new model of service provisioning in distributed systems encourages researchers to investigate its benefits and drawbacks on executing scientific applications such as workflows. One of the most challenging problems in clouds is workflow scheduling, i.e., the problem of satisfying the QoS requirements of the users as well as minimising the cost of workflow execution. In this paper, a novel meta-heuristic method, called chemical reaction optimisation (CRO), is developed to solve deadline-constrained workflow scheduling, which tries to minimise the cost of workflow execution while meeting a user-defined deadline. A set of appropriate parameters can be obtained based on orthogonal experimental design (OED) and factor analysis. Experiments are done in two real workflow applications, and the results demonstrate the effectiveness of the proposed algorithm.