In this study, we conduct ambient noise tomography and teleseismic two-plane-wave tomography to probe the crustal and uppermost mantle structures in the Middle-Lower Yangtze River region. The data used include 14 months (from July 2012 to August 2013) of continuous vertical component ambient noise data and 219 teleseismic earthquakes recorded at 138 broadband seismic stations from Chinese provincial networks and 19 temporary seismic stations deployed by China University of Geosciences (Beijing). First, we apply ambient noise tomography to the collected ambient noise data to generate Rayleigh wave group and phase velocity maps at 5-42 s periods and applied two-plane-wave tomography method to earthquake data to generate intermediate-to-long period phase velocity maps at 20-143 s periods. We then combine the short-to-intermediate period velocity maps from ambient noise and the intermediate-to-long period phase velocity maps from earthquake data to generate broadband phase velocity maps at periods from 5 to 143 s. By inverting these 5-143 s Rayleigh wave velocity maps, we construct a 3-D shear wave velocity model from the surface to ~250 km depth in the Middle-Lower Yangtze River region. The 3-D model shows that in the upper crust, the basin regions, including the JiangHan, HeHuai, SuBei, HeFei and NanYang basins, are all featured with low velocities, and the mountain regions with high velocities. In the uppermost mantle, a low-velocity zone at ~100-200 km depth is observed beneath the Middle-Lower Yangtze River Metallogenic Belt. Moreover, our tomographic results show that the NingWu and NingZhen ore districts are clearly characterized by the strongest low velocity anomaly in the uppermost mantle at ~70-200 km depth. The depth extent of the low-velocity zone becomes shallower and the amplitude of low velocity anomaly becomes larger from the southwest JiuRui ore district to northeast NingWu ore districts. The change pattern of the low-velocity zone in the depth extent and the amplitude is consistent with the fact that peak ages of magmatic events along the Middle-Lower Yangtze River Metallogenic Belt progressively become younger and younger from 148 Ma in the southwest to 125 Ma in the northeast. The observed low-velocity zone may represent the cooling hot upper mantle which was partially molten in the past resulting from partial melting of the paleo-Pacific plate or of an enriched mantle source induced by the westward subduction of the paleo-Pacific plate. The upwelling of the mantle-derived magmas may result in the formation of these granitic rocks and coeval ores deposits along the Middle-Lower Yangtze River Metallogenic Belt.