The crystal formation in urea–formaldehyde (UF) resin of low formaldehyde/urea (F/U) mole ratio generates a poor adhesion at the expense of low formaldehyde emission. Therefore, this study investigated the way to prevent the crystallization in cured UF resin by mixing 5% of nanoclay during the addition reaction of resin’s synthesis. Montmorillonite (MN) and laponite (LN) were used as the nanoclay. X-ray diffraction (XRD) and Fourier Transform Infrared (FTIR) results showed that the chemical structure of pristine nanoclay-UF resins was still crystal, while modified MN-UF resin was partially amorphous. In addition, modified LN-UF resin was still crystal, similar with that of pristine nanoclay-UF resin. The neat UF resin had a crystallinity of about 54.1% after curing. But, after the addition of nanoclay during resin’s synthesis, the crystallinity of cured UF resin remarkably decreased to 29.3% using modified MN and 47.5% using modified LN. This eventually improved the adhesion and reduced formaldehyde emission of plywood bonded with UF resin. These results showed that the prevention of crystallization in UF resin could be done by mixing 5% modified MN during the synthesis, which subsequently improved the adhesion strength by 33.6% (1.37 MPa) and lowered the formaldehyde emission by 56.1% (0.73 mg/L). The modified MN was intercalated in UF resin polymers during synthesis and eventually partially blocked the crystal formation in cured UF resins. This could facilitate the formation of three-dimensional cross-linking structures in cured UF resin and led to a better adhesion strength and reduced formaldehyde emission of plywood bonded modified UF resin.