A method and apparatus (100) for cleaning semiconductor wafer are provided, combining batch cleaning and single wafer cleaning together. The method includes the following steps: tacking at least two wafers from a cassette in a load port (110) and putting said wafers into a first tank (137) filled with chemical solution; after said wafers have been processed in the first tank (137), taking said wafers out of the first tank (137) and keeping said wafers in wet status; putting said wafers into a second tank (138) filled with liquid; after said wafers have been processed in the second tank (138), taking said wafers out of the second tank (138) and keeping said wafers in wet status; putting one of said wafers on a chuck inside a single wafer cleaning module (150); rotating the chuck while applying chemical solution on said wafer; applying deionized water on said wafer; drying said wafer; taking said wafer out of the single wafer cleaning module (150) and then putting said wafer back to the cassette in the load port (110).