Contaminant source identification and hydraulic conductivity estimation are of great significance for contaminant transport model in the subsurface media, but their actual values are difficult to obtain and can usually be inversely identified and estimated by sparse observations. In order to reduce computational cost in the process of estimating groundwater model parameters, the surrogate model was often used. This study addresses this challenge by proposing a modified self-organizing map (SOM) based surrogate model, named ILUES-SOM. The proposed model combines a modified iterative ensemble smoother method (SGSIM-ILUES) and the SOM algorithm to simultaneously identify contaminant source parameters and hydraulic conductivity field. Considering the characteristics of the proposed method (ILUES-SOM), a comparison of parameter estimation accuracy and computational efficiency is performed with the original SOM and SGSIM-ILUES inversion model. Moreover, the robustness of ILUES-SOM model for inversion was illustrated by proposing varying degrees of observation errors and missing early observation data. The results indicated that ILUES-SOM model can successfully retrieve unknown contaminant source simultaneously with heterogeneity hydraulic conductivity field in the groundwater system.