In the context of partial entanglement entropy (PEE), we study the entanglement structure of the island phases realized in several 2-dimensional holographic set-ups. From a pure quantum information perspective, the entanglement islands emerge from the self-encoding property of the system, which gives us new insights on the construction of the PEE and the physical interpretation of two-point functions of twist operators in island phases. With the contributions from the entanglement islands properly taken into account, we give a generalized prescription to construct PEE and balanced partial entanglement entropy (BPE). Here the ownerless island region, which lies inside the island \text{Is}(AB)Is(AB) of A\cup BA∪B but outside \text{Is}(A)\cup \text{Is}(B)Is(A)∪Is(B), plays a crucial role. Remarkably, we find that under different assignments for the ownerless island, we get different BPEs, which exactly correspond to different saddles of the entanglement wedge cross-section (EWCS) in the entanglement wedge of A\cup BA∪B. The assignments can be settled by choosing the one that minimizes the BPE. Furthermore, under this assignment we study the PEE and give a geometric picture for the PEE in holography, which is consistent with the geometric picture in the no-island phases.