Myelin water fraction (MWF) mapping with a multi-echo gradient echo (mGRE) sequence using complex-value based model fitting approach was recently described, in which the phase of the data plays an important role in the accuracy of the fitting results. Thus, influences coming from the undesirable phase components need to be reduced. Targeted for improved MWF mapping, methods to combat these phase related issues which include offset correction, main magnetic field (B0) inhomogeneity related correction, and flow compensation have been developed. For offset correction, a coil combine method with bipolar readout gradients has been devised. For B0 related artifact, a voxel spread function correction approach along with a navigator echo acquisition was utilized. Finally, flow compensation gradients were used to reduce the effects of flow from regions including the veins. The correction methods led to reduced residual fitting error and improved quality of the resultant MWF maps. Quantitative analysis shows increased reliability when the corrections were used. Data from normal volunteers showed improved MWF mapping with the integrated method developed in this work.