Methods on using the test results of in situ shear wave velocity to determine the category of engineering sites that has been disturbed or transformed by humans have not been discussed in relevant codes or documents. Based on the revelation of engineering site category and the summary of actual experience for many years, this paper gives the theoretical basis and a practical method to solve the problem. It is necessary to evaluate whether the scope and depth of the disturbance is big enough to influence the effect of seismic waves on the site. The evaluation is done on the basis of site volume disturbed by humans. If the volume is large enough, for example, a three-dimensional block with a range of about 1 km² and a depth of tens of meters, it is necessary to determinate the site category using in situ test shear wave velocity. If the volume of the site is not large enough, for example, only local disturbance, the in situ wave velocity cannot be directly used; the average wave velocity of disturbed layer should be replaced by 85% of the wave velocity in 1 m range below the disturbed layer. The reason is that a small amount of disturbance is not large enough to change the engineering category of the site but it may change the results of the in situ wave velocity test, thus leading to misjudgment.