Non-destructive testing of plant organs, tissues, and cells has important implications in studying the immediate physiological status of plants. The portable dynamic ion flux test equipment (PDIFTE) was developed based on Fick’s first law of diffusion and the Nernst equation to achieve the ion flux measurement in pmol cm−2s−1. This equipment integrates micro-imaging, micro-signal processing, automation and control, and biosensor technologies with the original signal acquisition and conditioning module, the motion control module, the macro 3D automatically control platform, micro digital imaging system, electrostatic shielding coating, ion-selective microelectrode, and other components. PDIFTE can detect H+, K+, Na+, Mg2+, Ca2+, Cd2+, Cl−, $$ {\text{NO}}_{3}^{ - } $$, and $$ {\text{NH}}_{4}^{ + } $$. This device can be used in the physiological mechanism research of salt-resistant, drought-resistant, cold-tolerant, heavy metal-resistant, and disease-resistant plants. It can also be used in the research on plant nutrition, ion channel-related gene function, and crop resistant breeding screening.