In this work, the spreading and dilution (mixing) processes of the miscible compound were analyzed numerically by three-dimensional Lattice Boltzmann Method (LBM) at a pore scale in a non-uniform flow field. The authors proposed an aperture-related dilution index to quantify the local dilution process in the different aperture regions. The results showed that the fluctuation of the compound spreading caused by the flow fluctuation depended on both the aqueous diffusivity and the frequency of the flow fluctuation. The flow fluctuation increased remarkably the original dilution index when the aqueous diffusivity of the miscible compound was relatively low. However, the analysis of the aperture-related dilution index showed that the degree of the dilution in smaller aperture regions was less than that in larger aperture regions, indicating that there was more incomplete dilution (mixing) in the smaller aperture region.