This paper summarizes the research in the field of modelling and simulation of complex systems conducted in recent years at the Department of Modelling and Simulation of Riga Technical University under the supervision of the corresponding member of the Latvian Academy of Sciences, Prof., Dr.habil.sc.ing. Yuri Merkuryev (Jurijs Merkurjevs). The main attention is devoted to developments within integrated simulation methodologies that incorporate simulation with other scientific approaches for the analysis, optimisation and management of complex systems, with a special focus on logistics systems. Practical application of the developed methods is considered by referencing to implemented research projects. Future research directions are also discussed.