Using the complex stratigraphic structure model, we study the changes in remaining oil on the millimeter scale in different structural parts during the different water flooding development methods. According to the actual geological structure characteristics of the oil layer, We designed and produced the meter-level experimental model, which ensures the similarity between the model structure and actual oil layer structure. The recovery rate of the primary water flooding stage is 10.36%. The stage recovery rate addition of the change flow direction stage is 7.85%. The final recovery rate is 41.36%. The physical interlayer structure has an influence on the oil saturation change in the nearby layers. The oil saturation reduction value is highest in the left part of layer 3 in the primary water flooding stage, the reduction range is 24.81%. There are 2 parts and 1 part where the oil saturation decreases by more than 10.0% in the second boost flooding stage and the change flow direction stage, respectively.