This study focuses on the reservoir scaling and the under-injection issues of the water injection well during the water injection development of an ultra-low permeability reservoir in Xinjiang due to the complex composition of injected water. Microfluidic experiments were applied to visualize the flow channel changes during water flooding, indoor core flooding experiments were employed to analyze the permeability and ion concentration, and nuclear magnetic resonance (NMR) was used to evaluate the pore structure damage. Together, these experiments were used to clarify the scaling and precipitation characteristics as the injected water met the formation water in porous media and the effects on reservoir damage. The research results showed that the poor compatibility of the injected water with the formation water could easily produce calcium carbonate scaling. The scaling products exhibited a unique network structure of blocks and a radial distribution, mainly composed of calcium carbonate and aluminosilicate. The scaling in the porous media exhibited the characteristics of unstable crystal precipitation, migration, and repeated scaling following water mixing, while the scale crystal growth occurred in the pores and the throats. According to the scaling characteristics, the damage to the reservoir permeability by scaling can be divided into the induction, damage, and stabilization stages. The filling and clogging of the scale crystals enhanced the pore structure heterogeneity, with the median pore radius reduced by 21.61% and the permeability reduced by 50%.