As a well-known transcription factor, Homeobox A10 (HOXA10) regulates a large number of downstream target genes, leading to the proper function development of endometrium for embryo implantation. The change of HOXA10 gene expression level can alter the expressions of many other genes, including coding and noncoding transcripts. In our study, mRNA and LncRNA expression profiles screening was performed by microarray when the HOXA10 gene expression level increased in Ishikawa cells. A total of 907 mRNAs and 1,026 LncRNAs were identified as differentially expressed transcripts (Fold Change ≥2, P-value <0.05, and Q-value <0.05) between HOXA10 overexpressed and control Ishikawa cells. Further analysis identified that these mRNAs participated in various biological processes, such as blood vessel development, cell adhesion, cell cycle, etc. Also, 14 enhancer-like LncRNAs and 108 LincRNAs with their nearby mRNAs were identified as coregulated transcripts. Our results showed that the mRNA and LncRNA expression profiles differed significantly between the two groups and provided useful information for further studying the molecular mechanisms of HOXA10 in endometrium.