This paper presents zircon U-Pb ages, whole-rock major and trace element data, and Sr-Nd-Hf isotopic compositions for the greenschists from the Heilongjiang Complex in NE China. Based on the geochronological and geochemical characteristics, the greenschists from the Heilongjiang Complex can be categorized into three series: Early Permian tholeiitic series (275 ± 1 Ma and 273 ± 1 Ma), Middle Permian alkaline series (261 ± 1 Ma), and Early Jurassic alkaline series (179 ± 1 Ma). The Early Permian tholeiitic greenschist samples are characterized by remarkable negative Nb and Ta anomalies, and they exhibit relatively low whole-rock (87Sr/86Sr)i values (0.703896–0.704252), along with positive εNd(t) values (+7.66 to +8.65) and positive εHf(t) values (+0.92 to +11.51), implying that their protoliths originated from the partial melting of a depleted mantle wedge that has been metasomatized by subducted slab fluids. The Middle Permian alkaline greenschist samples have high Nb (17.3–19.0 ppm), TiO2 (1.40–1.64 wt%), and P2O5 (0.60–0.68 wt%) concentrations, and they are enriched in large ion lithophile elements and light rare earth elements, and depleted in high field strength elements and heavy rare earth elements, with high whole-rock (87Sr/86Sr)i values (0.709434–0.709949), negative εNd(t) values (−4.73 to −4.72) and varied εHf(t) values (−10.11 to +4.86), which compositionally align with those of Nb-enriched basalts. Based on the geochronological and geochemical characteristics, we propose that the protolith generation of Middle Permian alkaline greenschists was associated with the partial melting of a mantle wedge that had been metasomatized by subduction slab-derived melts. The Early Jurassic alkaline greenschist samples display OIB affinities, characterized by whole-rock (87Sr/86Sr)i values ranging from 0.705161 to 0.705926, εNd(t) values between +6.16 and +6.19, and εHf(t) values from +3.44 to +9.32, indicating the formation of the protolith for the Early Jurassic alkaline greenschist was related to the upwelling of the asthenosphere resulting from slab break-off. By integrating regional geological data, we can trace the subduction evolution of the Mudanjiang Ocean back to the Early Permian, and the slab break-off during the Early Jurassic likely corresponded to the early stage of the closure of the Mudanjiang Ocean.