Growth mode and surface structures of the Pb/Si(001) system have been investigated by scanning tunneling microscopy. The growth mode is the Stranski-Krastanov type and Pb grows layer by layer up to three layers before three dimensional (3D) nucleation of Pb islands occurs. The structure of the first layer changes from 2X2 and 2X1, passing through intermediate phases of 2X4 and c(8X4) with mixing by increasing Pb coverage. The second layer is a 2X1 structure, and the third layer is a c(4X4) structure. 3D islands of triangular shapes grow on the third layer of c(4X4) in an orientation of Pb(111)Si(001) at coverages higher than 2 monolayers.