We investigate whether depositional sequences can form on 1000 y or millennial scale, and what stratal architecture can develop as the result of these short term variations. Abrupt climate changes are caused by a complex interplay between atmospheric, oceanic, and cryospheric processes. Dansgaard-Oeschger (D-O) cycles of ∼ 1000 y and Bond cycles of ∼ 7000 y have been identified in climate studies since the early 1990s. A 3D forward stratigraphic model, Dionisos, was used in this study to analyze the possible stratigraphic architecture that may evolve in response to the millennial-scale climatic cycles. According to current knowledge, no detectable eustatic changes occur in a D-O cycle, but sea level may change slightly through several D-O cycles. An abrupt ∼ 20 m fall and subsequent rise characterize the Heinrich events between Bond cycles. Our modeling included three experiments: (i) stable sea level, (ii) slightly rising sea level, and (iii) slightly falling sea level between Heinrich events. The applied fluvial water discharge and sediment supply varied according to the millennial climatic variations in each experiment. The modeling experiments lead to the formulation of a conceptual model for millennial-scale stratigraphy relevant to glacial periods. The millennial-scale sequences belong to a two-fold hierarchy defined by a series of short D-O cycles nested within longer Bond cycles, which, in turn, are separated by the sharp Heinrich events. The stacking patterns predicted between Heinrich events include: (i) alternating thicker and thinner bedsets of normal regressive highstand progradation (HST) on D-O scale, if sea level is stable; (ii) highstand systems tract–transgressive systems tract (HST-TST) sequences on D-O scale, if the sea level is rising; and (iii) thickening and thinning forced regressive bedsets on D-O scale, if the sea level is falling. In case iii, the Bond-scale falling-stage systems tract (FST) has two distinct parts: a proximal slightly and gradually downstepping unit, followed by a strongly offlapping unit deposited offshore. The intra-FST surface that separates the two units corresponds to the Heinrich sea-level drop, and is referred to in this paper as the “Heinrich discontinuity.” This type of sequence consists of FST-LST-TST, and no HST may form.