This study investigated fatigue crack propagation rates in the base metal (BM), heat affected zone (HAZ) and weld metal (WM) of a double-sided electron beam welded (EBW) joint of Ti alloy with a thickness of 140 mm in different layers. Firstly, this research measured fatigue crack propagation rates at different zones in each layer of the joint and drew curves thereof. The results demonstrate that the WM in the second layer of the double-sided EBW joint shows poor resistance to fatigue crack propagation. Secondly, the metallographic microstructures of different zones in different layers of the joint were observed. It is found that there are a lot of needle-shaped martensites growing in a specific direction at the HAZs in different layers of the joint. Finally, precipitates in different zones in each layer of the joint were studied by using a high-resolution scanning electron microscope (SEM). The results show that needle-shaped martensites in the WM of the joint are interlaced and present basketweave microstructures, while there are needle-shaped, lamellar martensites at the HAZs in each layer of the joint.