The research is dedicated to the development of methods and algorithms for a simulation-based fitness landscape analysis and optimisation of complex systems. Research is motivated by a wide spread of hard optimization problems nowadays and a relevance of improvement of their solution methods. Application of the fitness landscape analysis methods in the engineering field and tasks of simulation-based optimisation are reviewed and analysed in the paper. A formalised scheme of simulation-based optimisation enhanced by fitness landscape analysis is developed. Strength and weakness of the fitness landscape analysis is researched on the benchmark landscapes, both with relations between efficiency of the optimisation algorithm and structural features of the corresponding fitness landscapes. The prototype of a software tool for the fitness landscape analysis of simulation optimisation problems is developed. Approbation of the developed methods is performed in optimisation of vehicle schedule and routes in the delivery planning task. Various metaheuristic optimisation scenarios with application of the fitness landscape analysis are investigated.