The nucleation and crystallization of glass-ceramics are typically influenced by early phase separation, which can impact glass properties. However, it has been challenging to characterize the nanoscale phase separation and understand the nucleation mechanism of lithium disilicate (L2S) glass-ceramics, which has resulted in some controversy. Here, we raised the direct evidence of nanoscale clustering in the glassy phase prior to formal nucleation and crystallization by element distribution. Firstly, the amorphous Li3PO4 phase formed on the boundary between the phase separation area and residual glass matrix, and then nucleation tended to start on this phase boundary. Furthermore, the effect of phase-separation on nucleation and final crystallize products was illustrated. By sufficient phase-separation, the formation of desired Li2Si2O5 and LiAlSi4O10 microcrystals was effectively motivated, which is prerequisite for high mechanical properties and transparency. We hope this work provides guidance to rationally understand the early phase separation in glass for subsequent controlling crystallization.