In this review article, we first briefly introduce the transport theory and quantum molecular dynamics model applied in the study of the heavy ion collisions from low to intermediate energies. The developments of improved quantum molecular dynamics model (ImQMD) and ultra-relativistic quantum molecular dynamics model (UrQMD), are reviewed. The reaction mechanism and phenomena related to the fusion, multinucleon transfer, fragmentation, collective flow and particle production are reviewed and discussed within the framework of the two models. The constraints on the isospin asymmetric nuclear equation of state and in-medium nucleon–nucleon cross sections by comparing the heavy ion collision data with transport models calculations in last decades are also discussed, and the uncertainties of these constraints are analyzed as well. Finally, we discuss the future direction of the development of the transport models for improving the understanding of the reaction mechanism, the descriptions of various observables, the constraint on the nuclear equation of state, as well as for the constraint on in-medium nucleon–nucleon cross sections.