For the purpose of characterizing geologically stored $$\text{ CO}_{2}$$ including its phase partitioning and migration in deep saline formations, different types of tracers are being developed. Such tracers can be injected with $$\text{ CO}_{2}$$ or water, and their partitioning and/or reactive transfer from one phase to another can give information on the interactions between the two fluid phases and the development of their interfacial area. Kinetic rock–water interactions and geochemical reactions during two-phase flow of $$\text{ CO}_{2}$$ and brine have been incorporated in numerical simulators (e.g., Xu et al., TOUGHREACT User’s Guide: A Simulation Program for Non-isothermal Multiphase Reactive Geochemical Transport in Variably Saturated Geologic Media. LBNL Report 55460, V.1.2., Berkeley, CA, 2004). However, chemical equilibrium between the fluid phases is typically assumed, and multi-component, multiphase, non-isothermal codes for $$\text{ CO}_{2}$$ –brine systems that incorporate kinetic mass transfer of tracers between the two fluid phases are not readily available. New models or further developments of existing models are therefore needed to provide the capability for interpreting the signals of novel tracers, including tracers with kinetic/time-dependent interface transfer. This paper presents such new numerical model of tracer transport in a non-isothermal two-phase flow system. The model consists of five different governing equations describing liquid phase (aqueous) flow, gas ( $$\text{ CO}_{2})$$ flow, heat transport and the movement of the tracers within the two phases, as well as allowing kinetic transport of the tracers between the two phases. A finite element method is adopted for the spatial discretization and a finite difference approach is used for temporal discretization. Some special technologies and solution strategies are adopted for increasing the convergence, ensuring the numerical stability and eliminating non-physical oscillations. The new numerical model is validated against the code TOUGH2/ECO2N as well as some analytical/semi-analytical solutions. Good agreement between the simulated and analytical results indicates that the model has capability to simulate two-phase flow and tracer transport in a non-isothermal two-phase flow system with high confidence. Finally, the capability to model transport and kinetic mass transfer of tracers between the two fluid phases is demonstrated through examples.