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Paeonia ostii 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 P. ostii, the changes of leaf physiological indicators and leaf microstructures of sole-cropping and intercropping P. ostii were investigated. P. ostii that intercropping cultivated under Illinois pecans (Carya illinoinensis (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 P. ostii 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 P. ostii under C. illinoinensis were significantly decreased, whereas the leaf relative water content was higher. Moreover, compared to sole-cropping, intercropping P. ostii under C. illinoinensis 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 (Pn) and transpiration rates (Tr). Notably, the reduction of high-temperature damage on intercropping P. ostii under C. illinoinensis with 4 m × 4 m rowing spaces was more significant than that under C. illinoinensis with 4 m × 8 m rowing spaces. This research provides some reference values for efficient plantation of P. ostii in the middle and lower reaches of the Yangtze River in China. [ABSTRACT FROM AUTHOR]