Cretaceous mafic dykes in Fujian province, SE China provide an opportunity to examine the nature of their mantle source and the secular evolution of the Mesozoic lithospheric mantle beneath SE China. The mafic rocks have SiO2 ranging from 47.42 to 55.40 wt %, Al2O3 from 14.0 wt % to 20.4 wt %, CaO from 4.09 to 11.7 wt % and total alkaline (K2O+Na2O) from 2.15 wt % to 6.59 wt %. Two types are recognized based on their REE and primitive mantle-normalized trace element patterns. Type-A is the dominant Mesozoic mafic rock type in SE China and is characterized by enrichment of light rare earth elements (LREE) ((La/Yb)n = 2.85–19.0) and arc-like trace element geochemistry. Type-P has relatively flat REE patterns ((La/Yb)n = 1.68–3.43) and primitive mantle-like trace element patterns except for enrichment of Rb, Ba and Pb. Type-A samples show EMII signatures on the Sr-Nd isotopic diagram, whereas type-P rocks have high initial 143Nd/144Nd ratios (0.5126–0.5128) relative to the type-A rocks (143Nd/144Nd = 0.5124–0.5127). The type-A rocks have 207Pb/204Pb ranging from 15.47 to 15.67 and 206Pb/204Pb from 18.26 to 18.52. All the type-A rocks show a negative correlation between 143Nd/144Nd and 206Pb/204Pb ratios and a positive relationship between 87Sr/86Sr and 206Pb/204Pb ratios, indicating mixing of a depleted mantle source and an EMII component. Geochemical modelling shows that the parental magmas were formed by 5–15 % partial melting of a spinel lherzolite, and contaminated by less than 1 % melt derived from subducted sediment. The type-P magmas were derived from a mantle source unmodified by subduction components. The wide distribution of type-A dykes in SE China suggests that subduction-modified lithospheric mantle was extensive beneath the Cathaysia Block. Geochemical differences between Mesozoic and Cenozoic mafic rocks indicate that lithospheric thinning beneath SE China occurred in two episodes: firstly by heterogeneous modification by subducted components in early Mesozoic times, and later by chemical–mechanical erosion related to convective upwelling of the asthenosphere during Cenozoic times.