Dispersion-flattened dispersion-decreased all-normal dispersion (DFDD-ANDi) photonic crystal fibers have been identified as promising candidates for high-spectral-power coherent supercontinuum (SC) generation. However, the effects of the unintentional birefringence of the fibers on the SC generation have been ignored. This birefringence is widely present in nonlinear non-polarization maintaining fibers with a typical core size of 2 µm, presumably due to the structural symmetry breaks introduced in the fiber drawing process. We find that an intrinsic form-birefringence on the order of 10−5 profoundly affects the SC generation in a DFDD-ANDi photonic crystal fiber. Conventional simulations based on the scalar generalized nonlinear Schrödinger equation (GNLSE) fail to reproduce the prominent observed features of the SC generation in a short piece (9-cm) of this fiber. However, these features can be qualitatively or semi-quantitatively understood by the coupled GNLSE that takes into account the form-birefringence. The nonlinear polarization effects induced by the birefringence significantly distort the otherwise simple spectrotemporal field of the SC pulses. We therefore propose the fabrication of polarization-maintaining DFDD-ANDi fibers to avoid these adverse effects in pursuing a practical coherent fiber SC laser.