Abstract We systematically construct flipped SU ( 5 ) × U ( 1 ) X models without and with bulk vector-like particles from F-theory. To realize the decoupling scenario, we introduce sets of vector-like particles in complete SU ( 5 ) × U ( 1 ) multiplets at the TeV scale, or at the intermediate scale, or at the TeV scale and high scale. To avoid the Landau pole problem for the gauge couplings, we can only introduce five sets of vector-like particles around the TeV scale. These vector-like particles can couple to the Standard Model singlet fields, and obtain suitable masses by Higgs mechanism. We study gauge coupling unification in detail. We show that the U ( 1 ) X flux contributions to the gauge couplings preserve the SU ( 5 ) × U ( 1 ) X gauge coupling unification. We calculate the SU ( 3 ) C × SU ( 2 ) L unification scales, and the SU ( 5 ) × U ( 1 ) X unification scales and unified couplings. In most of our models, the high-scale or bulk vector-like particles can be considered as string-scale threshold corrections since their masses are close to the string scale. Furthermore, we discuss the phenomenological consequences of our models. In particular, in the models with TeV-scale vector-like particles, the vector-like particles can be observed at the Large Hadron Collider, the proton decay is within the reach of the future Hyper-Kamiokande experiment, the lightest CP-even Higgs boson mass can be increased, the hybrid inflation can be naturally realized, and the correct cosmic primordial density fluctuations can be generated.