Disruption of the alveolar barrier can trigger acute lung injury. This study elucidated the association of methyltransferase‐like 3 (METTL3) with Streptococcus pneumoniae (SP)‐induced apoptosis and inflammatory injury of alveolar epithelial cells (AECs). AECs were cultured and then infected with SP. Furthermore, the expression of METTL3, interleukin (IL)‐10, IL‐6, tumor necrosis factor‐alpha (TNF‐α), monocyte chemoattractant protein‐1 (MCP‐1), long noncoding RNA nuclear paraspeckle assembly transcript 1 (NEAT1), mucin 19 (MUC19), N6‐methyladenosine (m6A), and NEAT1 after m6A modification were detected by qRT‐PCR, Western blot, and enzyme‐linked immunosorbent, m6A quantification, and methylated RNA immunoprecipitation‐qPCR analyses, respectively. Moreover, the subcellular localization of NEAT1 was analyzed by nuclear/cytosol fractionation assay, and the binding between NEAT1 and CCCTC‐binding factor (CTCF) was also analyzed. The results of this investigation revealed that SP‐induced apoptosis and inflammatory injury in AECs and upregulated METTL3 expression. In addition, the downregulation of METTL3 alleviated apoptosis and inflammatory injury in AECs. METTL3‐mediated m6A modification increased NEAT1 and promoted its binding with CTCF to facilitate MUC19 transcription. NEAT1 or MUC19 overexpression disrupted their protective role of silencing METTL3 in AECs, thereby increasing apoptosis and inflammatory injury. In conclusion, this is the first study to suggest that METTL3 aggravates SP‐induced cell damage via the NEAT1/CTCF/MUC19 axis.