We investigate the phenomenology of a model based on the SU(3)⌄c × SU(3)⌄L × U(1)ₓ gauge theory, the so-called 331 model. In particular, we focus on the Higgs sector of the model which is composed of three SU(3)⌄L triplet Higgs fields and is the minimal form for realizing a phenomenologically acceptable scenario. After the spontaneous symmetry breaking SU(3)⌄L × U(1)ₓ → SU(2)⌄L × U(1)ᵧ, our Higgs sector effectively becomes that with two SU(2)⌄L doublet scalar fields, in which the first- and the second-generation quarks couple to a different Higgs doublet from that which couples to the third-generation quarks. This structure causes the flavor-changing neutral current mediated by Higgs bosons at the tree level. By taking an alignment limit of the mass matrix for the CP-even Higgs bosons, which is naturally realized in the case with the breaking scale of SU(3)⌄L × U(1)ₓ much larger than that of SU(2)⌄L × U(1)ᵧ, we can avoid current constraints from flavor experiments such as the B⁰ − B̅⁰ mixing even for the Higgs bosons masses that are O(100) GeV. In this allowed parameter space, we clarify that a characteristic deviation in quark Yukawa couplings of the Standard Model–like Higgs boson is predicted, which has a different pattern from that seen in two Higgs doublet models with a softly broken Z₂ symmetry. We also find that the flavor-violating decay modes of the extra Higgs boson, e.g., H/A → tc and H^± → ts, can be dominant, and they yield the important signature to distinguish our model from the two Higgs doublet models.