The Dixon method is frequently employed in clinical and scientific research for fat suppression, because it has lower sensitivity to static magnetic field inhomogeneity compared to chemical shift selective saturation or its variants and maintains image signal-to-noise ratio (SNR). Recently, research on very-low-field (VLF < 100 mT) magnetic resonance imaging (MRI) has regained popularity. However, there is limited literature on water-fat separation in VLF MRI. Here, we present a modified two-point Dixon method specifically designed for VLF MRI. Most experiments were performed on a homemade 50 mT portable MRI scanner. The receiving coil adopted a homemade quadrature receiving coil. The data were acquired using spin-echo and gradient-echo sequences. We considered the T2* effect, and added priori information to existing two-point Dixon method. Then, the method used regional iterative phasor extraction (RIPE) to extract the error phasor. Finally, least squares solutions for water and fat were obtained and fat signal fraction was calculated. For phantom evaluation, water-only and fat-only images were obtained and the local fat signal fractions were calculated, with two samples being 0.94 and 0.93, respectively. For knee imaging, cartilage, muscle and fat could be clearly distinguished. The water-only images were able to highlight areas such as cartilage that could not be easily distinguished without separation. This work has demonstrated the feasibility of using a 50 mT MRI scanner for water-fat separation. To the best of our knowledge, this is the first reported result of water-fat separation at a 50 mT portable MRI scanner.