Sandblasted, large‐grit, and acid‐etched (SLA) titanium (Ti) with microtopography is currently one of the most widely used implant materials to accelerate osseointegration. Numerous long noncoding RNAs (lncRNAs) have been involved in bone remodeling, with their role in osseointegration, and the underlying mechanisms remain largely unclear. Here, microarrays of human bone marrow mesenchymal stem cells (hBMSCs) were used to identify differentially expressed lncRNAs during early cell differentiation stages (0–7 days) on SLA Ti and polished Ti surfaces. The function of lncRNAs in the osteogenic differentiation of hBMSCs was identified by RNA silencing and overexpression assays. RT‐PCR and Western blot were used to detect RNA and protein expression. Alkaline phosphatase (ALP) protein activity was tested by ALP staining. Altogether, 4112 differentially expressed lncRNAs were identified from day 0 to day 7 on SLA Ti with a novel lncRNA, Prader‐willi region non‐coding RNA 1‐209 (PWRN1‐209) upregulated. We then proved that PWRN1‐209 promoted osteogenic differentiation in hBMSCs by genetic tools. The upregulation of PWRN1‐209 was further confirmed to be related to the surface topography of Ti by comparing SLA Ti and polished Ti. Interestingly, this trend seems to have a certain correlation with the mRNA expression level of integrins (α2, αV, β1, β2) and the phosphorylation of focal adhesion kinase (FAK). Taken together, the lncRNA PWRN1‐209 was upregulated by the SLA microtopography Ti surface, which may regulate osteogenic differentiation of hBMSCs through integrin‐FAK‐ALP signaling. Our results provide new insights into the relationship between surface topography and osseointergration.