Abstract: Nankun Railway runs from Nanning to Kunming through Yungui Plateau with total length of 863km,and height difference of 2000m. The geomorphic features differ along the line and bring a great difficulty in the project construction, many regions are connected by bridges and tunnels. The exposed rock layers, from Upper Proterzoic to Cenozoic deposits are located on the southwestern border of Yangtze paltform where folds are densely distributed, active faults longly, extend and seismic intensity reaches Ⅸ. The complication of regional geology and geological structure induces many geologic hazards, especially for the segment which runs 400km long through a carbonate rock region, where the karst is developed. These are found at the engineering foundations of bridges, tunnels and embankments. So, a large anount of engneeing design was taken. Furthermore embankment engineering was badly hindered by the long, highly expandable expansion rock. The way chosen and the effective measures taken for the complicated engineering geological conditions are discussed in this paper.