Cardiac hypertrophy refers to an abnormal increase in the thickness of the heart muscle. Our study explores the role of Krüppel-like factor 9 (KLF9) in hypertrophic obstructive cardiomyopathy (HOCM)-induced cardiomyocyte hypertrophy, providing new targets for the treatment of HOCM. Cardiomyocytes were treated with isoproterenol (ISO). The levels of natriuretic peptide B (BNP)/natriuretic peptide A (ANP)/KLF9/long non-coding RNA urothelial carcinoma-associated 1 (lncRNA UCA1)/p27 were measured. Cell surface area and protein/DNA ratio were tested. The binding between KLF9 and the lncRNA UCA1 promoter and between zeste homologue 2 (EZH2) and lncRNA UCA1 was verified. The enrichment of histone H3 lysine 27 tri-methylation (H3K27me3) and EZH2 on the p27 promoter was analysed. ISO treatment increased KLF9 and lncRNA UCA1 expression and decreased p27 expression in cardiomyocytes. KLF9 knockdown inhibited ISO-induced cardiomyocyte hypertrophy, reduced ANP and BNP expression, and alleviated cardiomyocyte damage. KLF9 activated lncRNA UCA1 expression. LncRNA UCA1 recruited EZH2 to the p27 promoter region, increasing the enrichment of H3K27me3, thereby epigenetically suppressing p27 expression. LncRNA UCA1 overexpression or p27 downregulation reduced the protective effect of KLF9 downregulation on cardiomyocyte hypertrophy. In conclusion, KLF9 activates lncRNA UCA1 expression, and lncRNA UCA1 epigenetically suppresses p27 expression, thereby exacerbating cardiomyocyte hypertrophy in HOCM.