When reservoir prediction is carried out in a deep-water carbonate-distributing area without any exploration well, it is commonly not only easy to judge reservoir-free bioherms erroneously as real organic reefs only according to the mound seismic reflection configuration that is considered as the proof of reef existence but also easy to ignore the shoal flats without the feature of mound seismic reflection which are likely to be reservoirs. Contrasting seismic reflection with seismic velocity in feature, it is shown that some deference and correlation exist among reefs, bioherms and shoal flat bodies. A reef is characteristic of the mound reflection configuration with high velocity, and a bioherm is of same mound reflection configuration but with low velocity while a shoal flat (body) is of high velocity without the mound reflection configuration. Based on such features, a new method is built for predicting reef reservoirs and shoal flat reservoirs in deep-water areas. This method is applied to predict once more the middle Miocene Meishan carbonate reservoir in some deep-water area of Qiongdongnan Basin. The re-prediction gives a different result that a large part of reefs that were predicted before into "reefs" are reclassified into bioherms and meanwhile shoal flats with a such large area nearly as the distribution area of the reefs are unexpectedly discovered. It is proved that it is an accurate method for predicting carbonate reservoirs in deep-water area.