Various germanium-based nanostructures have recently demonstrated outstanding lithium ion storage ability and are being considered as the most promising candidates to substitute current carbonaceous anodes of lithium ion batteries. However, there is limited understanding of their structure and phase evolution during discharge/charge cycles. Furthermore, the theoretical model of lithium insertion still remains a challenging issue. Herein, we performed comparative studies on the cycle-dependent lithiation/delithiation processes of germanium (Ge), germanium sulfide (GeS), and germanium oxide (GeO2) nanocrystals (NCs). We synthesized the NCs using a convenient gas phase laser photolysis reaction and attained an excellent reversible capacity: 1100-1220 mAh/g after 100 cycles. Remarkably, metastable tetragonal (ST12) phase Ge NCs were constantly produced upon lithiation and became the dominant phase after a few cycles, completely replacing the original phase. The crystalline ST12 phase persisted through 100 cycles. First-principles calculations on polymorphic lithium-intercalated structures proposed that the ST12 phase Ge12Lix structures at x ≥ 4 become more thermodynamically stable than the cubic phase Ge8Lix structures with the same stoichiometry. The production and persistence of the ST12 phase can be attributed to a stronger binding interaction of the lithium atoms compared to the cubic phase, which enhanced the cycling performance.