The invention provides an isothermal amplification system and method of a fluorescence self-inhibition probe. The isothermal amplification system comprises a combination of two fluorescence self-inhibition probes, a Vent DNA polymerase, an Nt.BstNBI nicking endonuclease, a buffer solution, a reaction raw material and miRNA target molecules. The fluorescence self-inhibition probes comprise a fluorescence self-inhibition linear probe and a fluorescence self-inhibition hairpin probe. The invention also provides an amplification method of the isothermal amplification system. According to the fluorescence self-inhibition probe isothermal amplification system and the amplification method, background fluorescence signals of the probe can be remarkably reduced, the detection signal-to-noise ratio is greatly increased, and detection of trace miRNA targets in a sample is facilitated. Meanwhile, no complementary sequence exists between the two background-free fluorescent probes, mismatching and extension between the probes can be prevented, the detection specificity is effectively improved, false positive results are avoided, and the system and method are particularly suitable for direct detection of miRNA molecular markers in clinical samples.