The difficulty in synthesizing guest-free semiconductor clathrates complicates the process of determining how these cage-like structures form. This work studies the microscopic mechanism of the nucleation of guest-free Si136 clathrate using molecular dynamics simulations with the Stillinger–Weber potential. The homogeneous nucleation of Si136, which is realized in a narrow negative pressure range before liquid cavitation, exhibits the characteristic feature of the two-dimensional (2D) mode. The critical nucleus is composed of one to two five-membered rings, and the nucleation barrier is close to 1 kBT. According to a thermodynamic model based on atomistic nucleation theory, the effective binding energy associated with the formation of 2D critical nuclei is significantly low, which is responsible for the low nucleation barrier of Si136 clathrate. In the post-nucleation period, the critical nucleus preferentially grows into a dodecahedron, and the latter continuously grows with sharing face along 〈1 1 0〉.