Based on the drilling data of six typical sites in Longtoushan town and the test data of dynamic nonlinear characteristics of soil, the seismic response analysis models of the corresponding sites were established respectively. Under the action of ground motion acceleration in east-west direction obtained by Longtoushan town strong observation station (053LLT) during Ludian earthquake with half-amplitude, the equivalent linearization method of one-dimensional soil layer seismic response analysis was used to calculate the seismic response of each site and the effect of near-surface overburden soil layer on peak acceleration. Response spectrum of ground motion was also discussed, and the relationship between site effect and earthquake damage was analyzed.