At present, soil arsenic contamination is one of the prominent environmental problems. The arsenic concentration in honeysuckle exceeds the standard levels, thus affecting the quality of traditional Chinese medicine. In this study, the hydroponic method was employed to explore the effect of organic arsenic (dimethyl arsenic) and trivalent inorganic arsenic (NaAsO2) on the growth of honeysuckle plants. The study demonstrated that low concentrations of inorganic arsenic (10−20 mg/L) and 10−50 mg/L organic arsenic had a stimulating effect on the growth of honeysuckle plants. The activities of antioxidant enzymes (peroxidase and catalase) increased correspondingly. However, the antioxidant system in honeysuckle plants was damaged under high concentrations of inorganic arsenic (20−40 mg/L) and 50−70 mg/L organic arsenic. On exposure to 30 mg/L NaAsO2 or 50 mg/L dimethyl arsenic acid for 10 days, the activities of peroxidase and catalase, as well as the malondialdehyde content, increased with prolonged exposure. The micro X-ray fluorescence analysis revealed that the accumulated arsenic in the roots was transported from the central vascular cylinders to the outer part of the root with the increase in concentration and exposure duration of inorganic arsenic. However, organic arsenic stress did not result in significant variations in the distribution of arsenic with increasing concentrations of arsenic. The arsenic element was predominantly located in the middle woody part of the root. The distributions of arsenic in the stems and leaves, in terms of organic and inorganic arsenic stresses, were similar, with accumulation primarily in the cortex of the stem and veins of the leaves. As a commonly used bulk traditional Chinese medicine, honeysuckle has a wide range of product quality issues. Hence, exploring the absorption, distribution, and transport trends of heavy metals such as arsenic in the plant body is of great significance for scientifically evaluating the impact of heavy metal pollution on the quality of medicinal materials and exploring ways to reduce the accumulation of heavy metals in the medicinal parts of plants.