A layered boron nitride (BN)–carbon nitride (CN) composite has been successfully synthesized by calcinating a mixture of BN nanoparticles and urea at 600 °C, wherein CN is formed from the thermal polymerization of urea during the calcination process. TEM analyses confirm that the BN-CN composite has a layered structure, being different from the morphologies of BN nanoparticles and CN. FTIR, XRD, and NMR results support that the layered BN-CN composite is most likely formed via the dehydration reaction between the -OH groups in the BN nanoparticles and the -NH2 groups in CN during the calcination process, which links BN nanoparticles and CN together to form the layered composite. The layered BN-CN composite can, with high efficiency, remove Neutral Red (NR) and Malachite Green (MG) from water (NR removal quantity: 1350.1 mg/g, concentration: 220 mg/L; MG removal quantity: 1040.6 mg/g, concentration: 120 mg/L), whereas the layered BN-CN composite has low efficiency to remove Methyl Orange (MO), Methylene Blue (MB), and Crystal Violet (CV) from water. The quantities of MO, MB, and CV removed are all just around 60 mg/g with a concentration of 120 mg/L. NR and MG are both protonated dyes, and their positive charges are from the bound H+. The layered BN-CN composite has high affinity for H+, which can cause the pH of the deionized water to increase to 8.89 from the initial 6.82. This may be responsible for the high removal efficiency of the layered BN-CN composite for NR and MG. Furthermore, the layered BN-CN composite can selectively remove NR (or MG) from NR-MO and NR-MB solutions (or MG-MO and MG-MB solutions).