In order to unravel the relationship between the root morphology, yield and quality of pepper under different aeration amounts and irrigation amounts, with groundwater of 5mg/L dissolved oxygen concentration in water (C) as controls, and two aeration rates of dissolved oxygen concentration at 15mg/L(A) and dissolved oxygen concentration at 40mg/L (O), and two irrigation amounts of 0.8 times- of crop-pan coefficient (W1) and 1.0 times croppan coefficient (W2) were set up by randomized block experiments. And correlation analysis and principal component analysis were coupled and used to analyze the optimal irrigation mode. Results showed that aerated irrigation significantly promoted pepper root morphology, yield, quality, plant height and nitrogen use efficiency. The yield of treatment AW1 was the highest at 6.78t/hm2, the yield of treatment AW1 was increased by 39.04% and 42.89% compared with that of OW1 and CW1 treatments, and the yield of treatment AW1 was increased by 30.80% compared with that of AW2 treatment （P<0.05). Compared with CW1, the soluble sugar content (BRIX), soluble protein content and sugar-acid ratio (SAT) of AW1 were increased by 29.49%, 75.24% and 68.10%（P<0.05), respectively, and the root dry weight, total root length, root volume and root surface area of AW1 were increased by 13.63%, 11.09%, 59.47% and 61.67%（P<0.05), respectively. At the same time, compared with the CW2 treatment, the height, nitrogen uptake, yield and irrigation water use efficiency of AW2 pepper plants were increased by 17.88%, 66.56%, 26.28% and 26.12%（P<0.05), respectively. Root morphology index, including root dry weight, total root length, root volume and root surface area, was significantly positively correlated with nitrogen uptake, plant height, yield, BRIX content, and soluble proteins content, and the comprehensive score of AW1 treatment were ranked first. In summary, from the aspects of quality improvement, yield increase and water saving, the treatment at the aeration rate of 15mg/L and the irrigation rate of 0.8 times the crop-pan coefficient was the best irrigation mode.