Nano-sized titanium dioxide (nTiO₂) is one of the most commonly used materials, however the knowledge about the molecular basis for metabolic and physiological changes in phytoplankton is yet to be explored. In the present study we use a combination of targeted metabolomics, transcriptomics and physiological response studies to decipher the metabolic perturbation in green alga Chlamydomonas reinhardtii exposed for 72 h to increasing concentrations (2, 20, 100 and 200 mg L^-1) of nTiO₂ with primary sizes of 5, 15 and 20 nm. Results show that the exposure to all three nTiO₂ materials induced perturbation of the metabolism of amino acids, nucleotides, fatty acids, tricarboxylic acids, antioxidants but not in the photosynthesis. The alterations of the most responsive metabolites were concentration and primary size-dependent despite the significant formation of micrometer-size aggregates and their sedimentation. The metabolic perturbations corroborate the observed physiological responses and transcriptomic results and confirmed the importance of oxidative stress as a major toxicity mechanism for nTiO₂. Transcriptomics revealed also an important influence of nTiO₂ treatments on the transport, adenosine triphosphate binding cassette transporters, and metal transporters, suggesting a perturbation in a global nutrition of the microalgal cell, which was most pronounced for exposure to 5 nm nTiO₂. The present study provides for the first-time evidence for the main metabolic perturbations in green alga C. reinhardtii exposed to nTiO₂ and helps to improve biological understanding of the molecular basis of these perturbations.