A semi-Dirac cone refers to a peculiar type of dispersion relation that is linear along the symmetry line but quadratic in the perpendicular direction. It was originally discovered in electron systems, in which the associated quasi-particles are massless along one direction, like those in graphene, but effective-mass-like along the other. It was reported that a semi-Dirac point is associated with the topological phase transition between a semi-metallic phase and a band insulator. Very recently, the classical analogy of a semi-Dirac cone has been reported in an electromagnetic system. Here, we demonstrate that, by accidental degeneracy, two-dimensional phononic crystals consisting of square arrays of elliptical cylinders embedded in water are also able to produce the particular dispersion relation of a semi-Dirac cone in the center of the Brillouin zone. A perturbation method is used to evaluate the linear slope and to affirm that the dispersion relation is a semi-Dirac type. If the scatterers are made of rubber, in which the acoustic wave velocity is lower than that in water, the semi-Dirac dispersion can be characterized by an effective medium theory. The effective medium parameters link the semi-Dirac point to a topological transition in the iso-frequency surface of the phononic crystal, in which an open hyperbola is changed into a closed ellipse. This topological transition results in drastic change in wave manipulation. On the other hand, the theory also reveals that the phononic crystal is a double-zero-index material along the x-direction and photonic-band-edge material along the perpendicular direction (y-direction). If the scatterers are made of steel, in which the acoustic wave velocity is higher than that in water, the effective medium description fails, even though the semi-Dirac dispersion relation looks similar to that in the previous case. Therefore different wave transport behavior is expected. The semi-Dirac points in phononic crystals described in this work would offer new ways to manipulate acoustic waves with simple periodic structures. Copyright © 2014 by ASME.