An efficient simplified isotope dilution method was developed to determine four carboxyl containing phytohormones simultaneously in 200 mg of fresh tomato tissues using ultra high performance liquid chromatography–triple quadrupole mass spectrometry (UPLC-MS/MS) with negative electrospray ionization. The four phytohormones are indole-3-acetic acid (IAA), abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA). Only one purification step of Oasis MAX solid phase extraction (SPE) was employed to enrich target phytohormones after crude extraction. In addition, two endogenous isomers of JA, (−)-JA and (+)-7-iso-JA, were separated directly. The validated method has been applied to monitor changes of JA, SA, IAA, and ABA in both local and systemic leaves of wild-type and transgenic 35S::prosystemin (35S::PS) tomato lines. Meanwhile, the JA burst amplified by the overexpressed prosystemin in 35S::PS was verified. Furthermore, the spatial and temporal changes of JA, SA, ABA, and IAA were analyzed.