By solving the Milburn equation, we investigate the thermal entanglement properties of a two-qubit Heisenberg XY chain in the presence of intrinsic decoherence. The controls of nonuniform magnetic field, the initial state of two qubits, the relative phases and the amplitudes of the polarized qubits on thermal entanglement are studied. The results show that for a particular initial state, the thermal entanglement can be increased by the external magnetic field. The time behavior of the entanglement exhibits a strong dependence on the initial state of two qubits, and it can be manipulated by changing the relative phase and the amplitudes of the polarized qubits. It is also notable that stable entanglement, which is dependent on initial state of the qubit, occurs even in the presence of decoherence. The magnetic field may have a constructive effect on the stable entanglement for a certain initial state, and the Bell-diagonal state turns out to be a dark state of the system in the absence of the magnetic field.