Room-temperature phosphorescence (RTP) materials have attracted wide interest due to their long lifetime and free from background autofluorescence. Nevertheless, simultaneous activation of stable long-lived RTP emission in both solid and aqueous phases remains a tremendous challenge. Herein, a molten salt method to synthesize boron carbon oxynitride nanodot-based RTP composites (BCNO nanodots@pyrophosphate) was carried out by employing pyrophosphate as the inert shell for BCNO nanodots. The BCNO nanodots@pyrophosphate1 with the average size of 3.69 nm show bright-green RTP because the introduction of phosphorus is beneficial to the intersystem crossing process and increases the RTP emission. What is more, whether in solid or aqueous dispersion, BCNO nanodots@pyrophosphate1 retains good phosphorescent properties with a high phosphorescence quantum yield (29.5% and 18.6%) and a long lifetime (1.39 and 1.29 s), which lasts over 15 s to the naked eye. This is the first report on BCNO nanodots with RTP in aqueous solution. The unique RTP characteristics allow BCNO nanodots@pyrophosphate as a hopeful indicator for detection of latent fingerprints with high contrast and multilevel information protection.