High-resolution single channel shallow-seismic profiles were used to analyze the Holocene sedimentation off the Minjiang River Estuary. The base surface of the Holocene is an erosional surface of MIS 2, locally paleo-river channels. Its depth is usually between 30 m and 60 m with the maximum of 65 m below present sea level. Generally, the surface is shallower near the shore and deeper toward the open sea, locally showing strips of negative topography due to paleo-river channels. The Holocene consists of marine depositional unit (U1) formed after late Early Holocene and fluvial-lacustrine-swamp depositional unit (U2) of early Holocene. The former unit is in turn composed of offshore-shallow sea parallel seismic facies and estuary-inshore clinoform seismic facies. Their landward onlap and seaward downlap against base surfaces are indicative, combined with distribution characteristics of sediment thickness, of major sediment sources and their transport tendency. The thickness of the all Holocene sediment is usually between 10 m and 20 m, with the maximum of 38 m in paleo-river channel areas, but absent in the area between Mazu Archipalegos and Baiquan Archipalegos. The marine Holocene is a few meters to 20 m, with the maximum of some 25 m in the southeastern area (east of the Haitan Island). Since the Holocene transgressive, there were three main sediment sources. Sediments from the Taiwan Strait in south covered the southern part of the study area. Minjiang River-delivered suspended sediments deposited in the northern area, mainly toward NE to the open sea with a southerly tongue-branch near the mouth. Its modern depocenter located in the northern estuary, indicated by a thickness of more than 15 m of mud. The northeastern part of the area was affected by suspended sediments from Zhejiang-Fujian Costal Current. Four sedimentary zones are distinguished. They are sedimentary zone of Taiwan Strait source, sedimentary zone of Minjiang River source, northeastern mixture zone and non-sedimentation zone between Mazu Archipalegos and Baiquan Archipalegos. Their average sedimentary rates are about 0.8 mm/a, 1.0 mm/a, 1.1 mm/a and 0 mm/a, respectively. The non-sedimentation zone between Mazu Archipalegos and Baiquan Archipalegos was mainly controlled by a flowing of island-circling sediment.