This paper firstly selects three typhoon cases (SHANSHAN, YAGI, XANGSANE) which occurred in 2006, and analyzes the distribution characteristic of the normalized radar cross-section (NRCS, σo), which were received by QuikSCAT scatterometer in the case of rain effect. Secondly, in order to account for the effects of rain to σo, we follow the theory of atmospheric radiation transfer and introduce two different types of rain radiation transfer models (called SY model and AMSR model, respectively), then combine these two models with NSCAT2 GMF to produce an improved GMF suitable for the case of rain effect (called GMF+RAIN). Lastly, based on this GMF+RAIN, we use the ambiguity removal method which integrates 2DVAR (two-dimensional variational assimilation) with MSS (multiple solution scheme) to retrieve the YAGI and XANGSANE typhoon wind fields which had different intensity. The new approach which combines GMF+RAIN with 2DVAR+MSS improves the result, which further verifies the effectiveness of GMF+RAIN. This new approach also makes the scatterometer data more effective and valuable for application in the research of typhoon.