The interaction of low-order modes with photonic crystals (PhCs) has been a promising technique to increase light extraction efficiency (LEE) of LEDs. In this paper, numerical simulations based on the finite-difference time-domain method were carried out to explore different mechanisms that can effectively improve this interaction. The results showed that deeply etched PhCs have inefficient light extraction since they would decrease the effective thickness of the unetched layer and cut off some guided modes. By applying the AlxGa1-xN confining layer, the distribution of guided modes was changed. The cap layer mode was isolated from the GaN buffer, and larger LEE was achieved. Furthermore, dramatic increments with oscillations were found in the LEE by using embedded PhCs. Resonances of the Bloch mode localized within these PhCs, which caused the oscillations, were further modified by a shallow AlxGa1-xN confining layer. With the optimized parameters, over eightfold increment in LEE was achieved. In addition, dislocations caused by higher Al content and thicker AlxGa1-xN layer were avoided. This proposed structure could be a very promising candidate for high extraction efficiency LEDs.