Pinus yunnanensis Franch., one of the pioneer species of wild mountain afforestation in southwest China, plays an essential role in the economy, society and environment of Yunnan Province. Nonetheless, P. yunnanensis’ trunk twisting and bending phenomenon has become more common, which significantly restricts its use and economic benefits. In order to clarify the compositional differences between the straight and twisted trunk types of P. yunnanensis and to investigate the reasons for the formation of twisted stems, the present study was carried out to dissect the macroscopic and microscopic structure of the straight and twisted trunk types of P. yunnanensis, to determine the content of cell wall components (lignin, cellulose, hemicellulose), determine the content of endogenous hormones, and the expression validation of phytohormone-related differential genes (GA2OX, COI1, COI2) and cell wall-related genes (XTH16, TCH4). The results showed that the annual rings of twisted trunk types were unevenly distributed, eccentric growth, insignificant decomposition of early and late wood, rounding and widening of the tracheid cells, thickening of the cell wall, and reduction of the cavity diameter; the lignin and hemicellulose contents of twisted trunk types were higher; in twisted trunk types, the contents of gibberellin (GA) and jasmonic acid (JA) increased, and the content of auxin (IAA) was reduced; the GA2OX were significantly down-regulated in twisted trunk types, and the expressions of the genes associated with the cell wall, COI1, COI2, TCH4 and XTH16, were significantly up-regulated. In conclusion, the present study found that the uneven distribution of endogenous hormones may be an important factor leading to the formation of twisted trunk type of P. yunnanensis, which adds new discoveries to reveal the mechanism of the genesis of different trunk types in plants, and provides a theoretical basis for the genetic improvement of forest trees.