This study identified the membrane fouling of a two-stage RO process of the Bai-sha brackish water desalination plant facing serious fouling problems. Two membrane modules, one from each stage, were autopsied and diagnosed for the cause for the failure of the RO system. Different morphologies were exhibited on the fouled membrane. Results suggested that the fouling on the first-stage membrane tended to be organic and biological, while that on the second-stage membrane appeared to be scaling. Higher than 85% of the foulants on the first stage membrane were organic substances in opposed to the 5 to 8% of those on the second stage membrane. However, the total organic matter on the second stage membrane was more than that on the first stage one. The thick layer of sealants on the surface of the second-stage membrane was identified to be calcium carbonate of which the crystal was clearly seen in the SEM images. The scaling was thickest at the outlet of the membrane. Huge amount of microbes were found on both membranes. The FTIR results also suggested the existence of extracellular polymeric substance (EPS) on the first stage membrane. This study recommended that the recovery rate, pH and the potential for bio-fouling should be defined at the real operation.