The interception of irradiation by smog pollution and cloud cover associated with extreme rainfall events has become an increasingly important limiting factor in crop production in China. Little is known about the adaptation of carbon (C) allocation to periodic low irradiance in field conditions. The trehalose signaling pathway plays a critical role in adapting C allocation to the environment in crops but its importance in adaptation to low light in field conditions is not known. To determine the effects of low irradiance on C economy and maize yield, two commonly grown hybrids (LY-16 and ZD-958) were subject to three levels of shading (15 %, 50 %, and 97 %) for one week from V13 stage in two successive seasons. Shading led to yield loss mainly due to decreased kernel number, which was greater in LY-16 than ZD-958. Effects of shading on leaf area and photosynthesis were similar in both varieties. Starch levels in leaves were maintained, whereas total soluble carbohydrates were reduced up to fivefold by shading in both varieties. Shading increased the proportion of photoassimilate retained in leaves relative to reproductive organs. Carbohydrates in ears and stem were decreased by shading similarly in both varieties. Amongst the parameters measured, the main difference between LY-16 and ZD-958 associated with yield penalty was the expression of class II trehalose phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) genes which were increased due to shading in leaves and ears, particularly in ears of LY-16. It is concluded that altered C fixation and allocation by low irradiance limited ear growth at pre-anthesis. Activation of TPSII and TPP genes indicates that the trehalose pathway likely plays a role in ear development under low light and could be a target for yield improvement under such conditions as with other stresses.