The rapid development of mRNA vaccines during the COVID-19 pandemic has highlighted the critical role of lipid nanoparticles (LNPs) as delivery systems. The advantages of prefilled syringes (PFSs) in mRNA-LNP administration are widely recognized. The compatibility of mRNA-LNP drugs with tungsten in PFSs has not yet been investigated. In this study, we used polyadenylic acid (Poly A) as an mRNA model to conduct accelerated stability experiments under conditions of 4 °C, 25 °C, and light exposure, examining the effects of three tungsten sources (commercial salts or tungsten extracted from syringe pins) on the physicochemical properties of LNPs. Additionally, enhanced green fluorescent protein (eGFP)-mRNA and Poly A were compared to validate the changes in bioactivity. Our findings revealed that tungsten significantly increased the particle size and polydispersity index (PDI) of Poly A-LNPs, while reducing zeta potential and encapsulation efficiency. Transmission electron microscopy (TEM) further demonstrated that tungsten-induced structural damage to Poly A-LNPs. eGFP-LNPs spiked with 50 ppm tungsten extract completely lost activity after 6 weeks of storage at 25 °C, even though they exhibited greater physicochemical stability than Poly A-LNPs. Light exposure, while having no significant impact on physicochemical parameters, substantially diminished LNP bioactivity. Subsequent nucleic acid integrity testing of tungsten-spiked eGFP-mRNA revealed that tungsten caused minimal changes in physicochemical properties, such as particle size and PDI, under real-world conditions, but significantly compromised eGFP-mRNA integrity. This suggests that mRNA integrity, rather than physicochemical metrics such as particle size, PDI, or encapsulation efficiency, is the critical quality attribute determining mRNA-LNP bioactivity.