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The interferometric imaging radar altimeter (InIRA) on‐board Chinese Tiangong‐2 space laboratory is a Ku‐band interferometric radar whose major aim is to measure the wide‐swath ocean topography. Unlike traditional interferometric synthetic aperture radar (InSAR) aiming at measuring digital elevation model of land surface, Tiangong‐2 InIRA adopts small incidence angles and short baseline to get strong and high coherency reflections from ocean surface. The interferometric phase noise is a notable source of errors which limits the accuracy of the ocean height measurements. Compared with traditional InSAR, the height error of Tiangong‐2 InIRA shows different distribution pattern due to the absolutely small but relatively large variation incidence angles. This study gives a filtering method for interferometric phase generated with small incidence angles and short baseline. Non‐uniform windows are selected …