The Darss–Zingst peninsula at the southern Baltic Sea is a typical wave-dominated barrier island system which includes an outer barrier island and an inner lagoon. The formation of the Darss–Zingst peninsula dates back to the Littorina Transgression onset about 8,000 cal BP. It originated from several discrete islands, has been reshaped by littoral currents, wind-induced waves during the last 8,000 years and evolved into a complex barrier island system as today; thus, it may serve as an example to study the coastal evolution under long-term climate change. A methodology for developing a long-term (decadal-to-centennial) process-based morphodynamic model for the southern Baltic coastal environment is presented here. The methodology consists of two main components: (1) a preliminary analysis of the key processes driving the morphological evolution of the study area based on statistical analysis of meteorological data and sensitivity studies; (2) a multi-scale high-resolution process-based model. The process-based model is structured into eight main modules. The two-dimensional vertically integrated circulation module, the wave module, the bottom boundary layer module, the sediment transport module, the cliff erosion module and the nearshore storm module are real-time calculation modules which aim at solving the short-term processes. A bathymetry update module and a long-term control function set, in which the ‘reduction’ concepts and technique for morphological update acceleration are implemented, are integrated to up-scale the effects of short-term processes to a decadal-to-centennial scale. A series of multi-scale modelling strategies are implemented in the application of the model to the research area. Successful hindcast of the coastline change of the Darss–Zingst peninsula for the last 300 years validates the modelling methodology. Model results indicate that the coastline change of the Darss–Zingst peninsula is dominated by mechanisms acting on different time scales. The coastlines of Darss and the island of Hiddensee are mainly reshaped by long-term effects of waves and longshore currents, while the coastline change of the Zingst peninsula is due to a combination of long-term effects of waves and short-term effects caused by wind storms.