Panax notoginseng total saponins (PNS), the main bioactive components of the radix and rhizome of Panax notoginseng (Burk.) F.H. Chen, could treat eye disorders. For the treatment of ocular diseases, eye drops are the first choice with the most common, economic and good compliance. So we proposed that PNS might be able to treat inflammatory ocular surface diseases by eye drops based on its anti-inflammatory and antioxidant activities. The short elimination half-life (t1/2) and rapid elimination of PNS after oral or intravenous administration may limit its application for eye disorders. Meanwhile, there is a lack of pharmacokinetic study on trace amount of tear samples with PNS eye drops. Therefore, a simple and sensitive ultra-performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (UPLC-QqQ-MS/MS) method by multiple reaction monitoring (MRM) in positive ion mode was firstly developed and applied in the pharmacokinetic study of PNS in rabbit tears. Tears samples were prepared by protein precipitation using methanol. The linearity, limit of detection, limit of quantification, specificity, precision, repeatability, stability, recovery, and matrix effect have been investigated and passed their validation criteria. Compared with prior methods, this method has the advantages of rapid analysis, high sensitivity, simple sample preparation and less sample demands. The pharmacokinetic results indicated that PNS eye drops had a slower elimination and a longer t1/2 by topical ocular administration, which is expected to improve the success rate of eye drops in the treatment of anterior segment diseases. The ocular pharmacokinetics of PNS provides an experimental guidance and feasibility basis for in vivo effect verification of PNS eye drops in the future investigation.