In this study, we used 60dayold seedlings of Malus hupenensis as materials, and sets T₁ (5 000 r/min×3 h), T₂ (5 000 r/min×6 h), T₃ (10 000 r/min×3 h) and T₄ (10 000 r/min×6 h) hypergravity stress, with no hypergravity stress as the control (CK). We investigated the chlorophyll, soluble protein, malondialdehyde, proline contents and membrane permeability of the seedling leaves under the hypergravity stress and transcriptome analysis on them, to preliminary explore the transcriptome response mechanism of M. hupenensis under hypergravity stress. The results showed that: (1) the hypergravity stress caused the leaves of the M. hupenensis seedlings to change from a stretched growth state to a different atrophy growth state, and the T₄ showed a significant atrophy growth state. (2) Under hypergravity stress, the chlorophyll and malondialdehyde contents of the seedling leaves of M. hupenensis under T₃ and T₄ were significantly higher than that of CK, and there was no significant difference between CK, T₁ and T₂ treatments. The proline content of leaves under all hypergravity stresses were significantly higher than that of CK. The membrane permeability under T₄ was significantly higher than that of CK, and there was no significant difference between T₁, T₂, T₃ and CK. The soluble protein content is reduced to different degrees under each hypergravity stress, but it is not significantly different from CK. (3) The sample sequencing results shows, the sequence length of most transcripts is more than 1 000 nt, total of 37 725 accounting for 79.15% of all transcripts, and CK, T₂, T₄ samples and the corresponding new genes are dominated by transcripts with FPKM value <5.0, the number of transcripts were 21 412, 20 162, 22 368 and 1 352, 1 411 and 1 406 respectively, accounting for 45.78%, 43.10%, 47.82% and 81.45%, 85.00% and 84.70%, respectively. (4) GO function annotation and enrichment analysis show that there are obviously different ways of differentially expressed genes in GO enrichment classification, as the intensity of hypergravity stress increases. It implies that the response of M. hupenensis to hypergravity is complex, but it mainly focuses on transcription factor activity and protein dephosphorylation. (5) Differential transcription factor expression analysis shows the bZIP family, the WRKY family and the ERF family have a relatively large upregulation with the increase of the intensity of the hypergravity stress. Among them, the gene expression levels of the bZIP and WRKY transcription factor families all show an upregulation trend with the increase of the intensity of the hypergravity stress. However, the expression of MD01G1177100, MD08G1096000, and MD13G1130700 in the ERF family has a downregulation trend with the increase of the intensity of hypergravity stress. The research showed hypergravity stress caused varying degrees of damage to the seedlings of M. hupenensis, and the total chlorophyll, malondialdehyde, proline contents and membrane permeability of the leaves were all significantly affected. Therefore, the contents of chlorophyll, soluble protein, malondialdehyde and proline in the leaves of seedlings, and the membrane permeability can be used as indicators of resistance to hypergravity stress. The research speculated that the effects of hypergravity stress on the transcription factors of M. hupenensis are mainly concentrated in the family of WRKY, bZIP and ERF transcription factors. The results of this study lay a theoretical foundation for mining and screening candidate resistance genes.