This paper aims to understand the function of fructose-1, 6-bisphosphate aldolase (FBA) in drought resistace of apeseed (Brassica napus L.), to reveal the relationship between gene expression and photosynthetic index and yield under drought stress, and to provide a reference for the identification and improvement of drought resistance. The high drought-tolerant rapeseed 94005 as experimental materials, were treated with drought stress during the flowering stage and with normal irrigation as the control group. We measured the photosynthetic parameters and FBA enzyme activities of the leaves and analyzed the expression of FBA through real-time fluorescence quantitative PCR (RT-qPCR). The RACE method was used to get the full-length clone of FBA gene. The sequencing results were analyzed with bioinformatics. After rehydration, the plants growed until maturity and rapeseed yield was measured, meanwhile the relationship was analyzed between gene expression, physiological parameters, yield and so on. The results showed that the rapeseed yield and net photosynthetic rate (Pn), stomatal conductance (Gs), and transpiration rate (Tr) of the leaves were significantly decreased, fructose-1,6-bisphosphate aldolase activity and gene expression were increased with the drought stress level increasing. The intercellular CO₂ concentration (Ci) was decreased and water use efficiency (WUE) was significantly increased under lightly, moderate, and severe stress, while the Ci was increased and WUE was decreased under extreme stress. The correlation analysis showed that the net photosynthetic rate and yield had a significantly negative correlation with FBA activity and the expression of FBA. The full length of FBA was 1440bp, and the ORF was located in 60bp-1172bp, encoding a protein of 370 amino acids with a predicted molecular weight of 38.51 kD and isoelectric point of 6.92. Homology comparison indicated that FBA of rapeseed had a consistency over 87% with Arabidopsis FBA. The secondary structure prediction showed that FBA protein consisted of α-helix, random coil, extending chain, and β-corner, as well as the proportion of four kinds of secondary structural elements was 43.85%, 31.28%, 17.60%, and 7.26%, respectively. The net photosynthetic rate and yield of rapeseed were decreased under drought stress, and the decrease was greater with the enhancement of stress. FBA gene was closely related to drought stress. FBA gene mainly improved plant adaptability to drought stress by inhibiting photosynthesis rate, reducing of transpiration rate, promoting effect of glycolysis, and aerobic respiration under drought stress.