Unconventional water resources (e.g., saline water, etc.) for irrigation as a promising supplementary water source can alleviate the freshwater shortage in the agriculture of red soil areas in Southern China. It should be noted that the presence of soluble salt in this water source may have detrimental influences on soil water infiltration and crop growth. Understanding the effect of unconventional water irrigation (UWI) on water infiltration in red soil is important. Previous studies have shown that the salinity of UWI can alter soil hydraulic properties to change soil water movement in saline soils. However, the underlying mechanism and factors of water infiltration in red soil under UWI with different salinity levels remain limited. Therefore, a laboratory experiment (one-dimensional vertical infiltration experiment and centrifuge method) was conducted to evaluate the effect of UWI with different salinity levels [0 (the distilled water, CK), 1 (S1), 2 (S2), 3 (S3), 5 (S5), and 10 (S10) g L−1] on the soil water infiltration process, soil water characteristic curve (SWCC), soil water constants estimated using the SWCC, saturated and unsaturated hydraulic conductivity (KS and K) as well as the soil chemistry of soil profile [pH, electrical conductivity (EC), and Na+ and Cl− contents]. The primary factors of soil water infiltration were identified using stepwise regression and path analysis methods. The results showed that UWI salinity decreased water infiltration by 1.53–7.99% at the end of infiltration in red soil, following the order of CK > S1 > S5 > S2 > S3 > S10. Moreover, UWI could enhance soil water availability with an increase of 8.55–12.68% in available water capacity. In contrast, lower KS and K were observed in S1–S10, and there was a negative linear relationship between irrigation salinity and KS. UWI also produced the EC, Na+, and Cl− accumulations in the soil profile. As the salinity level of UWI increased, the accumulations aggravated. Soil acidification was found in S1–S5, while soil alkalization was observed in S10. Additionally, α, PWP, and KS were the primary factors influencing the water infiltration of red soil. This study can help optimize the soil infiltration model under UWI and establish a foundation for unconventional water management in the red soil regions of Southern China and other similar regions. In addition, the undisturbed red soil under agricultural unconventional water irrigation and the long-term effect of unconventional water application should be considered.