We present a full three-dimensional algorithm for time-domain fluorescence molecular tomography. A pair of appropriate transform-factors is employed to extract the featured information on the temporal profiles for time-domain coupled diffusion equations. The linear inversions at two distinct transform-factors are solved with an algebraic reconstruction technique,and the normalized Born ratio is proposed. The simulate phantom is measured in reflection and transmittance modes by use of multi-channel time-correlation single photon counting system. We experimentally validate that the proposed scheme can achieve simultaneous three-dimensional reconstruction of the fluorescent yield and lifetime. The results show that for the positions,sizes and shapes of the targets,there are some deviation in reflection measurement,the quality in transmittance one is better and in the two-mode is more satisfied.