Provided are nanofunctional silica particles having excellent functionality and quality, and capable of being mass-produced at low costs. According to the present invention, there are provided nanofunctional silica particles including a coating layer containing one or more silica compounds selected from the group consisting of mercaptopropyl trimethoxysilane (MPS), mercaptopropyl triethoxysilane (MPES), mercaptopropyl methyldimethoxysilane (MPDMS), trimethoxy[2-(7-oxabicyclo[4.1.0]-hept-3-yl)ethyl]silane (EpoPS), thiocyanatopropyl triethoxysilane (TCPS), acryloxypropyl trimethoxysilane (ACPS), and aminopropyl trimethoxysilane (APS) and functional particles in the coating layer, and being used in imaging, assay, diagnosis, treatment or the like, medicine or bioresearch.