Relatively large measurement uncertainty severely hindered wide application for laser-induced breakdown spectroscopy (LIBS), therefore it is of great importance to understand the mechanism of signal uncertainty generation, including initiation and propagation. It has been found that the fluctuation of plasma morphology was the main reason for signal uncertainty. However, it still remains unclear what mechanism leads to laser-induced plasma morphology fluctuation. In the present work, we employed three fast-imaging cameras to capture three successive plasma images from a same laser-induced Titanium alloy plasma, which enables us to understand more clearly of the plasma evolution process especially for the early plasma evolution stage when plasma and surrounding gases interact drastically. Seen from the images, the plasma experienced an increasing morphological fluctuation as delay time increased, transforming from a “stable plasma” before the delay time of 100 ns to a “fluctuating plasma” after the delay time of 300 ns. Notably, the frontier part of plasma showed a significant downward motion from the delay time of 150 ns to 200 ns and crashed with the lower part of the plasma, making the plasma flatter and later even splitting the plasma into two parts, which was considered as a critical process for the transformation of “stable plasma” to “unstable plasma”. By calculating the correlation coefficient of plasma image pairs at successive delay times, it was found that the higher the similarity between two plasma at early stage, the more similar at later stage; this implied that the tiny plasma fluctuation earlier than the critical delay time (150–200 ns) was amplified, causing a large plasma fluctuation at the later stage as well as LIBS measurement uncertainty. The initiation of slight fluctuation was linked with Rayleigh–Taylor Instability (RTI) due to the drastic material interpenetration at the plasma-ambient gas interface at earlier stage (before 50 ns). That is, the uncertainty generation of LIBS was proposed as: plasma morphology fluctuation was inevitably trigged by RTI at the early stage and the tiny fluctuation was amplified by the back pressed downward process of plasma frontier material, leading to severe morphology fluctuation as well as LIBS signal uncertainty.