Short answer: Refraction! When starlight passes through Earth’s atmosphere, layers of air at different temperatures refract the starlight, bending its path. The amount of bending is constantly changing with the wind, so the starlight forms a very faint dancing pattern on the ground, like the mottled light on the bottom of a swimming pool. As you look up through those bright and dark spots, the amount of starlight reaching your eyes changes, and you’ll see the star twinkle.

Long answer: You might have heard that the twinkling of the stars at night is caused by light pollution, or maybe dust grains high in the atmosphere. It’s actually neither– while both of those things can make it harder to see the stars by either blocking out their light (dust) or overwhelming their glow (light pollution), what makes the stars appear to twinkle and flash is refraction. Refraction is the same phenomena that makes the air shimmer above a hot car.
Think of it this way: when starlight passes through our atmosphere, it will encounter pockets of air at different temperatures, right? The starlight might shine through a cold wind at high altitude, hot heat waves rising from pavement, a warm inversion layer, cool air left over from a rainstorm earlier in the day… Well, one of the properties of a material is called the ‘refractive index’: it measures ‘how much does light bend when it enters this material’. As it turns out, the refractive index of air changes with temperature. So when the starlight passes through those pockets of different-temperature air, it gets bent around this way and that, almost like it’s passing through big lenses!
It’s really not a stretch to say that the atmosphere is full of big messy lenses moving around all over the place! When you think about it, air pockets work the same way as glass lenses. Both air and glass lenses are made of a clear material that has a refractive index which is different from their surroundings, so that the light will bend when it enters them. The difference is that the refractive index of glass is much bigger than the variation in refractive index of air; that’s why a small glass lens in a telescope can have WAY more magnification than a huge ‘air lens’ up in the atmosphere does.
Have you ever noticed a star near the horizon flashing with rainbow colors? You weren’t imagining things! The refractive index of a material is not only different for different temperatures of air, but also for different colors of lights. Red light bends less than yellow light, which bends less than green light, which bends less than blue light… So when a star is really twinkling like crazy, the different colors of light can become noticeably separated, and you’ll be able to watch the color flicker as well as the brightness.