The use of phosphogypsum as a cement-based filling material to replace cementitious materials is an effective comprehensive utilization. At present, there is a lack of systematic research on the internal pore distribution characteristics and the properties of carbonation and seepage resistance of phosphogypsum incorporated into concrete, which can easily lead to structural failure. In this paper, six groups of basalt fiber concrete specimens with different proportions of phosphogypsum content were prepared and tested for carbonation and seepage resistance, and the effect of different phosphogypsum content on the carbonation and seepage resistance of basalt fiber concrete was investigated by combining with XRD, SEM, and specific surface area and pore size analysis. The results show that the carbonation depth of basalt fiber concrete increases with the increase of phosphogypsum content and carbonation age, and there is a functional relationship between phosphogypsum content, carbonation age and carbonation depth. The water penetration height of basalt fiber concrete shows a trend of increasing first and then decreasing with the increase of phosphogypsum content. The microstructural analysis reveals that with the increase of phosphogypsum content, the specific surface area of basalt fiber concrete and pore volume of different pore sizes increase, and the amount of ettringite (AFt) increases. The increase of total pore volume leads to the increase of carbonation rate and water penetration height growth in the early stage. AFt has micro-expansion property, and the joint action of AFt and C-S-H gel to fill up some of the pore channels, which not only lead to the decrease of carbonation rate in the late stage of basalt fiber concrete, and the decrease of water penetration height in the phosphogypsum content more than 6% (mass fraction), but also lead to the decrease of specific surface area and pore volume of different pore sizes of basalt fiber concrete with 15% (mass fraction) phosphogypsum. The research results provide reference information for further enrichment and improvement of phosphogypsum resource utilization technology.