Based on the complete seven-volume framework of three-dimensional time field theory, this paper resolves two core unsolved problems of the Standard Model: the physical origin of exactly three generations of leptons and quarks, and the fundamental geometric mechanism of quark confinement. Spontaneous layered nested folding of the quantum time field produces three independent topological eigenstates, which naturally correspond to the three generations of elementary particles and reproduce the observed particle mass hierarchy without artificial parameter tuning or hypothetical new particles. The distorted quantum time field surrounding isolated quarks forms a closed topological flux-tube structure; linearly increasing field potential energy forbids free quark separation and causes mandatory hadronization, perfectly explaining the permanent confinement phenomenon in quantum chromodynamics. All microscopic particle behaviors are uniformly derived from the intrinsic spacetime topology of the 3DT system, maintaining full logical consistency with macroscopic cosmology, quantum gravity and fundamental interaction theories established in previous papers and completing the microscopic particle physical closure of the whole unified field system. AI Usage Note: All theoretical ideas, mathematical derivations and conclusions are independently created by the author. Generative AI was only used for linguistic polishing of sentences. The author takes full responsibility for all content.