  We investigate the phenomenology of a model based on the $SU(3)_c\times
SU(3)_L\times U(1)_X$ 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 this corresponds to the minimal form to realize
phenomenologically acceptable scenario. After the spontaneous symmetry breaking
$SU(3)_L\times U(1)_X\to SU(2)_L\times U(1)_Y$, 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 the different Higgs doublet from that
couples to the third generation quarks. This structure causes the flavour
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 $SU(3)_L\times
U(1)_X$ to be much larger than that of $SU(2)_L\times U(1)_Y$, we can avoid
current constraints from flavour experiments such as the $B^0$-$\bar{B}^0$
mixing even for the Higgs bosons masses being ${\cal O}(100)$ 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 $Z_2$ symmetry. We also find that the flavour violating decay
modes of the extra Higgs boson, e.g., $H/A \to tc$ and $H^\pm \to ts$ can be
dominant, and they yield the important signature to distinguish our model from
the two Higgs doublet models.
