The mechanism by which photosynthetic adaptation occurs in maize (Zea mays L.) during both drought and the subsequent recovery after re-watering is currently unknown. To elucidate this mechanism, two maize cultivars (drought tolerant SD609 and drought sensitive SD902) were subjected to an eight-day drought, followed by re-watering for four days. The photosynthetic electron transport rates and related gene expression were measured in both cultivars. Compared to control plants, progressive drought stress significantly decreased electron transport rates at the donor and acceptor sides of PSI and PSII in SD902, and of PSII in SD609. Meanwhile, the expression of cab, psbP, psbA, psbD, petA, and petB genes involved in electron transport system were significantly down-regulated in both cultivars, particularly in the SD902. Moreover, while expression of psaA and psaB genes encoding PSI was down-regulated in SD902, there were no changes in SD609 during drought stress. After re-watering, measured fluorescence parameters and key photosynthesis-related gene expression levels returned to near control values in SD609, but not in SD902. This finding indicated that SD609 was characterized by reversible down-regulation of PSII, while in SD902, an impairment occurred in two photosystems, and such coordination between PSII and PSI contributed to drought tolerance in SD609. Overall, the higher drought tolerance and rapid recovery capability of SD609 were associated with more effective self-regulation of photochemical activities and photosynthesis-related gene expression, which appears to represent a critical adaptive mechanism to withstand and survive the rapidly changing climate.