Tool design and working parameters for subsoiling in wet clayey paddy soil are different from those for dry land cropping system. Investigation on the subsoiling process and the governing mechanisms requires detailed description on the underlying influential factors. Field soil parameters were used as a reference to construct a DEM model for subsoiling which was suitable for wet clayey soil analysis and performed in a EDEM software. The proposed DEM model of clayey paddy soil was then implemented to simulate a subsoiling process, in which directly measured draft and macroscopic disturbance of field soil was compared. Microscopic process and mechanisms of soil fragmentation were assessed with simulated stages. Results showed that simulation error with the proposed DEM model was less than 6.63%. Mean error of the resulted microrelief was 4.39%. Mean error of elevated ridge was 19.22%. The measured results from microscopic approach were re-evaluated and the correctness of related assumptions from microscopic approach was confirmed by DEM results, soil failure boundary evolution and soil failure with particle contacting models were depicted. A soil fragmentation index was proposed for describing soil fragmentation behavior from DEM perspectives. The error of fragmentation index with respect to measured soil fragmentation parameter was less than 3.46%, affirming that the proposed parameter was a suitable tool for microscopic description of soil failure imposed by subsoiling. This research provides a powerful technical basis for the interaction mechanism between soil and soil, and lays a theoretical foundation for the optimization design of the soil contact parts.