In order to calculate the surface of the nanoparticles large size aggregate local electromagnetic fields distribution and to evaluate its effect, the scripting language is used to write the local and the grid in the software program to implement the nanoparticles large size aggregate model of discrete non-uniform grid, combined with the finite difference time domain (FDTD) method to implement three sizes aggregate model of electromagnetic field simulation. The K-means clustering algorithm is used to cluster the calculated electric field data, and finally the average enhancement factor is obtained which could reflect the electromagnetic enhancement effect at all “hot spots” locations of the large-size aggregation of gold nanoparticles. The results show that the memory usage of the sub-grid discrete gold nanosphere dimer simulation model is reduced by 81%, and the simulation speed is doubled, which effectively improves the simulation efficiency of FDTD. In addition, the enhancement factor AEF 2, which is the same as the average enhancement factor (AEF 1) calculated by traditional integration method, can be obtained by K-means clustering algorithm and electromagnetic data of the aggregate of gold nanoparticles of three sizes.