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<i>Paeonia ostii</i> is an emerging woody oil crop, but the high temperature in summer is extremely unfavorable for its growth and development. Understory intercropping cultivation would provide shaded environments which could effectively reduce the ambient temperature. In order to explore whether understory intercropping cultivation would reduce the effects of high-temperature stress on <i>P. ostii</i>, the changes of leaf physiological indicators and leaf microstructures of sole-cropping and intercropping <i>P. ostii</i> were investigated. <i>P. ostii</i> that intercropping cultivated under Illinois pecans (<i>Carya illinoinensis</i> (Wangenh.) K. Koch) with 4 m × 4 m and 4 m × 8 m rowing spaces were used as samples in this study. The results showed that with continuous high temperature, the high-temperature damage index of <i>P. ostii</i> kept increasing, whereas the leaf relative water content continued to decline. Compared to sole-cropping, the high-temperature damage index, relative electrical conductivity, proline content, antioxidant enzymes superoxide dismutase (SOD), and ascorbate peroxidase (APX) activities of intercropping <i>P. ostii</i> under <i>C. illinoinensis</i> were significantly decreased, whereas the leaf relative water content was higher. Moreover, compared to sole-cropping, intercropping <i>P. ostii</i> under <i>C. illinoinensis</i> increased SPAD and chlorophyll contents, made mesophyll cell ultrastructures more intact, and made the chloroplasts rounder and more filled with starch granules and lipid globules, leading to enhanced photosynthesis (<i>Pn</i>) and transpiration rates (<i>Tr</i>). Notably, the reduction of high-temperature damage on intercropping <i>P. ostii</i> under <i>C. illinoinensis</i> with 4 m × 4 m rowing spaces was more significant than that under <i>C. illinoinensis</i> with 4 m × 8 m rowing spaces. This research provides some reference values for efficient plantation of <i>P. ostii</i> in the middle and lower reaches of the Yangtze River in China.