Wood-based structure panels have been widely used in building construction, aerospace, and furniture industries, where adhesives bonding plays an essential role in the manufacturing processes. Formaldehyde-free adhesive resins are in high demand to meet the increasingly stringent environmental regulations and have sparked enormous research interest. This work reports a systematic investigation of bonding behavior of a pMDI adhesive delivered as a water/pMDI emulsion and used as a model system to investigate the adhesive penetration depth and resulting bonding strength when used as an adhesive to bond wood plies. The approach of water/pMDI emulsion can avoid a water distribution problem which has to be considered in a traditional procedure for bonding wood materials. The stability and phase separation of the water/pMDI emulsion system were first examined by image analysis and viscosity measurements as well as the effects of the emulsion composition on the bonding strength of the adhesive. By both the pull-off and lap-shear tests, it was determined that a water content around 30% by weight of the emulsion was providing optimum strength while yielding emulsions stable enough to be practically applied on wood surfaces. After this optimization, the adhesive penetration depth was altered by treating the wood surface with a silane agent (APTES) so as to improve the bonding strength. The results show that a moderate penetration helps enhance bonding strength, providing insights into the nonproportional relationship between adhesive penetration and bonding strength.