Using nitrogenous fertilizer is a basic way to increase agricultural output. Meanwhile, nitrogen removal by soil denitrification can dissipate the residual nitrogen that infiltrates into the soil, leading to protection groundwater from pollution. Factors influencing the measurement of nitrogen removal by soil denitrification are complicated and there are no relatively perfect methods for measurement wildly used at present. Based on discussion of essence and influence of denitrification in soil layers of aeration zone, the influence and deficiency of measuring method in use are analyzed in this paper. A system of methods of measuring denitrification in soil layers of aeration zone is tentatively suggested for groundwater protection. Something valuable for related scientific research is also provided.