While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling.