Fluorescence lifetime imaging microscopy (FLIM) enables detection of complex molecular assemblies within a single voxel for studies of cell function and communication with subcellular resolution in optically transparent tissue. We describe a fast FLIM technique consisting of a novel time-correlated single-photon counting (TCSPC) detector that features 80 MHz average count rate and the phasor analysis for efficient data acquisition and evaluation. This method in combination with multiphoton microscopy enables acquisition of a lifetime image every 1-2 s in 3D live organotypic tissue culture. 3D time-lapse fluorescence lifetime data were acquired over up to 20 h and analyzed by using exponential fitting and phasor analysis. By correlating specific areas in the phasor plot to the actual image, we obtained direct insight into cancer-cell invasion into a 3D collagen matrix, the differential uptake of doxorubicin by cells, and the consequences on cell invasion and apoptosis induction. Based on the fast acquisition and simplified image postprocessing and quantification, time-lapse 3D FLIM is a versatile approach for monitoring the 3D topography, kinetics, and biological output of structurally and spectrally complex cell and tissue models.