Here we report the synthesis of nucleoside α-P-boranodiphosphate analogs via our improved phosphoramidite approach, where the addition of a non-nucleophilic base, TEA, to deprotonate phosphorus is considered to be critical to improve final product yields. Protonation on trivalent phosphorus might not only have blocked Lewis acid borane modification, but also have promoted byproduct formation through a trans-nucleophile process. Here, based on 31P NMR data, mechanisms are proposed for P(V)P(III) bond cleavage via phosphorus protonation-promoted nucleophile-exchange, and TEA deprotonation of phosphorus in promoting product formation in anhydrous synthetic reaction mixtures.