Abstract: Taking five tomato lines as test materials, including ABA deficient mutant（LA0673） and its wild type（LA0535）,NCED overexpressing transgenic strain RD29 A:NCED1（#2,#7） and its wild type plant Mill.L.cv.New Yorker（WT）.Changes of tomato external morphology and related physiological indexes were studied by simulating waterlogging stress artificially, in order to understand the effect of ABA on photosynthetic physiology of tomato.The results showed that the leaves of LA0673 were wilting and showed a gray-green color, and there was no aerial roots in LA0673 under waterlogging stress, but there were a lot of aerial roots in the other 4 tomato lines; the root activity of five lines significantly decreased and LA0673 was dead at 7 days of waterlogging treatment, The root activity of LA0535 decreased to 6.34% of 0 day, 9.62% of #7,3.14% of WT and 6.43% of #2;LA0673 showed a significant increase in chlorophyll content due to wilting on the 7 days of flooding treatment, and the other 4 lines showed a downward trend, the chlorophyll content of LA0535 was 57.13% of 0 day, 60.98% of #7,60.67% of WT and 80.30% of #2;the net photosynthetic rate（Pn）,stomatal conductance（Gs） and transpiration rates（Tr） of five lines showed a downward trend; the Gs of LA0535,WT,#2 and #7 decreased immediately in the early waterlogging treatment, they were earlier than LA0673;the intracellular carbon dioxide concentration（Ci） of five lines increased significantly or stabilized at a high level.Combined with the observation of external morphological changes under waterlogging stress, it was suggested that ABA was closely involved in plant photosynthesis by regulating stomatal size; ABA improved waterlogging tolerance by promoting the aerial root or adventitious root formation of tomato.