Abstract: With the rapid development of human economic society, metro has been one of the most important facilities in cities. Dealing with complex karst problem during metro construction remains a great challenge, which has resulted in large investment. During the construction of the 6th line of Kunming rail transit project, serious mud loss and collapse of the holes occurred in the punching holes for the No.1 shield well envelop structures. Research on the engineering and hydrological geology is carried out by the use of drilling core experiments, cross hole electromagnetic wave tests, geological and hydrological observations. The research results in that the karsts are very commonly developed in the engineering area, which can be a reference for the karst investigation and for the design and construction of the metro lines in Kunming.