The invention provides an isonucleoside compound or an ortho-phosphite derivative thereof. The compound can be used for effectively increasing the gene silencing efficiency of oligonucleotide modified by the compound and keeping the enzyme stability of the oligonucleotide. The invention further provides a preparation method of the isonucleoside compound or the ortho-phosphite derivative thereof, a solid-phase synthesis method of oligonucleotide 5' end phosphorylation and the application of the compound to the modification of the oligonucleotide.