Investigations of soil microbial diversities in the Tarim desert highway shelter forest lands drip-irrigated with saline water with methods of Biolog-eco, PLFA and PCR-DGGE, and evaluation of the soil fertility qualities using integrated fertility index (IFI) method, were conducted in this work; the relationship between soil microbial diversity and IFI values were also revealed. The main results are below: (1) Notable differences on diversities of carbon metabolism, genetic gene and fatty acid were found among the sandy soils drip-irrigated with different saline water (F > F_0.05); The water with higher mineralization reduced the soil microbial activity. (2) The notably significant differences of soil IFI values were found among the forest lands with different plantation times (F > F_0.01); Meanwhile, the vertical variation of IFI values at the different soil layers were also markable (F>F_0.05), the value at 0-5 cm was the least, and the IFI value decreased with increase of mineralization of the saline water. (3) There were power function relationships between the soil IFI values and the soil microbial diversities of carbon mechanism, fatty acid, but polynomial relationship existed in the IFI value and the soil microbial genetic gene. So, microbe population would contribute greatly to increase soil fertility in the Tarim desert highway shelter forest lands under saline water drip-irrigation.