The invention discloses a wafer testing system and method. The system comprises a flying-probe tester and a carrier plate, the flying-probe tester is used for testing a wafer to be tested, the carrier plate is used for bearing the wafer to be tested on the flying-probe tester and providing an alignment mark corresponding to a clamping plate frame of the flying-probe tester and the domain of the carrier plate, the domain of the carrier plate and the domain of the wafer to be tested are matched to form a domain file to be tested, and after the domain file to be tested is led into a software operation system of the flying-probe tester, a testing figure file is formed. According to the wafer testing system and method, various pinboard wafers or wafers of passive integrated devices can be automatically tested through the flying-probe tester, an automatic probe table does not need to be bought for testing the wafer with different domains, corresponding expansive probe cards do not need to be customized according to the wafers to be tested with the different domains, the flexibility is improved, the cost is lowered, the period is shortened, and the industrialization process of the wafer pinboarrds such as TSV and TGV and an IPD technology is promoted.