In this paper, we investigate the physical layer discriminatory channel estimation (DCE) in multiple-input multiple-output (MIMO) decode-and-forward (DF) relay systems which comprise a source, a relay, a destination, and an eavesdropper node. In the first channel estimation phase (phase 1), the relay transmits a training signal while the source transmits a cooperative jamming signal omnidirectionally, such that the destination has a better estimation of the relay-destination channel while the eavesdropper has a poor estimation of the relay-eavesdropper channel. In the second channel estimation phase (phase 2), the source transmits a training signal while destination transmits a cooperative jamming signal through the null space of the relay-destination channel. That is, the estimation quality of the source-eavesdropper channel is seriously degraded by the jamming signal. In each channel estimation phase, we design the training signal and determine cooperative jamming power to discriminate the channel estimation performance between the legitimate receiver and eavesdropper. Numerical results illustrate that the proposed DCE scheme increases the mean square error (MSE) difference between the legitimate channel and eavesdropper channel in both phases.