Experimental investigation of subspace quantum process tomography in three-spin system was implemented via nuclear magnetic resonance. A quantum process was characterized by measuring a complete set of input states and corresponding outputs. The method using ancillary qubit remarkably reduces the number of the initial input states. And the pulse sequences used in this paper have fewer J-coupling evolutions. The experiment time was shortened and quantum decoherence of the system was weakened efficiently. ; Natural Science Foundation of Fujian Province, China [2008J0219]