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This study investigated the chronology of heterogeneous, multilayered, and overlapped architectures by combining experiments with computer simulations of thermoluminescence (TL) dating. We proposed a heterogeneous and multilayered model based on the cylindrical configuration for both excavated and buried status. The obtained results indicated that our model was able to determine the chronology of architectures having multilayered and overlapped structures, which differs from those obtained using the conventional spherical and homogeneous model from ten to several hundred years. Our proposed model also explicitly exhibited the significant contributions of excavation, destruction, and radiation shielding to the accurate determination of chronology. Application of the proposed model to the Oc Eo archaeological site in Vietnam suggested that the actual chronologies of four investigated architectures should be around AD 615–953, whereas the homogeneous model predicted their chronologies of about one to several decades older. In particular, our study provided the first scientific evidence for the formation of an overlapped architecture in an architectural assembly at the Oc Eo site, namely there was an (older) architecture constructed around AD 794 and lasted for about 159 years before being destroyed, probably by the kingdom's historical upheavals. Since then, another (younger) architecture was built on top of the older one's foundation. Our findings, which are also in good agreement with the radiocarbon dating using accelerator mass spectrometry (AMS), are crucial for archaeology as they provide solid evidences for the historical argumentations associated to the mysterious ancient Funan kingdom that spread across many countries in Southeast Asia, including Southern Vietnam. They also open a new research approach towards re-dating the chronologies of controversial complex architectures, which can change our understanding on the history of many nations in the world. • A heterogeneous and multilayered model with cylindrical configuration was proposed. • Computer simulation combined with field and laboratory experiments were conducted. • Chronologies of multilayered and overlapped architectures were precisely determined. • Chronologies of two overlapped structures in a single architecture were distinguished. [ABSTRACT FROM AUTHOR]