The development of nano drug delivery systems (NDDSs) provides new approaches to fighting against diseases. The NDDSs are specially designed to serve as carriers for the delivery of active pharmaceutical ingredients (APIs) to their target sites, which would certainly extend the benefit of their unique physi-cochemical characteristics, such as prolonged circulation time, improved targeting and avoiding of drug-resistance. Despite the remarkable progress achieved over the last three decades, the understanding of the relationships between the in vivo pharmacokinetics of NDDSs and their safety profiles is insufficient. Analysis of NDDSs is far more complicated than the monitoring of small molecular drugs in terms of structure, composition and aggregation state, whereby almost all of the conventional techniques are inadequate for accurate profiling their pharmacokinetic behavior in vivo. Herein, the advanced bio-analysis for tracing the in vivo fate of NDDSs is summarized, including liquid chromatography tandem-mass spectrometry (LC-MS/MS), F(o)rster resonance energy transfer (FRET), aggregation-caused quench-ing (ACQ) fluorophore, aggregation-induced emission (AIE) fluorophores, enzyme-linked immunosor-bent assay (ELISA), magnetic resonance imaging (MRI), radiolabeling, fluorescence spectroscopy, laser ablation inductively coupled plasma MS (LA-ICP-MS), and size-exclusion chromatography (SEC). Based on these technologies, a comprehensive survey of monitoring the dynamic changes of NDDSs in struc-ture, composition and existing form in system (i.e. carrier polymers, released and encapsulated drug) with recent progress is provided. We hope that this review will be helpful in appropriate application methodology for investigating the pharmacokinetics and evaluating the efficacy and safety profiles of NDDSs.