Despite the commercial achievement of heap leaching of some copper, gold, zinc, and nickel minerals, there is limited comprehension of the flow pattern within the heap. Several field investigations have suggested that bypassing of ore by leaching solution is a common phenomenon, and the leaching process was significantly influenced by it. The extraction and surface morphology of low-grade copper sulphides under the condition of preferential flow was investigated in this paper. The experiment result, conducted within a novel bioleaching apparatus, shown that majority of acid was consumed by alkaline gangue and matrix, so the concentration of Cu2+ and total Fe increased slightly at the initial leaching stage. The ore extraction decreased with the increasing of its location depth, for instance, the ore extractions of the top and bottom region were 29% and 2% respectively. Preferential flow happened within the fine region due to the low irrigation employed by this experiment, and the extraction of fine ores was larger than that of coarse ores. The SEM images showed that the surface of top ores within the column was degraded seriously, but the middle and bottom ores were attacked slightly. Plenty of cracks were observed on the bottom ore surface due to the precipitation layer of sulfur and jarosite.