Pokémon are different from humans in biological structure. In fact, their matter is unstable and has a certain tendency to turn into a special form of energy. This is, however, only triggered by certain radiation.
This radiation is that of Apricorns, those nut-like fruits people made Pokéballs out of in ancient times. The inside of an Apricorn's shell contains energy drainers, a sort of biological energy black holes - they let out that certain radiation and they can suck energy in to their centers. Those are there to protect the Apricorns from Pokémon that might want to eat them in a very effective way - a Pokémon that cracks the shell of an Apricorn will be hit by the radiation, turn into energy, and be sucked towards the Apricorn. This can imprison smaller Pokémon inside forever - which additionally provides the Apricorn with more power to suck in more Pokémon - or if it is a powerful Pokémon, it would feel dizzy and perhaps decide the Apricorn is not good to eat. If a Pokémon actually eats the Apricorn, however, it dies and the energy drainers release the energy they contained.
Different types of Apricorns, targeted as food for different kinds of Pokémon, contain different kinds of energy drainers which suck in different types of energy - usually some form which is dominant in some Pokémon and not others (such as Water Pokémon, fast Pokémon, heavy Pokémon, etc.). All Apricorns contain some drainers for all variations, though, so they can all catch anything that is weak enough. Humans also react to the radiation from the Apricorns, but are nowhere near as unstable as Pokémon and only long-term exposure to open Apricorns can cause any problems for humans. This, however, is what has happened to Kurt in G/S/C - it causes the person to seem older than what they really are.
Those who make Pokéballs out of Apricorns use special tools for it. They open the Apricorns, hollow them out and then close them with hinges that will, as regular Pokéballs, open upon semi-harsh impact with the ground or a Pokémon (hence the need to throw the balls). This, of course, greatly increases a Pokémon's chance to escape from the ball.
In a normal Pokéball, different types of mechanical energy drainers have been placed behind a few mirrors. The mirrors work like the glossy inside of an Apricorn's shell, reflecting the Pokémon so that it does not get divided between the energy drainers. They have different types so that the ball will have an equal chance of catching all Pokémon.
What the Pokémon experiences inside the ball is a sort of timeless, dreamy environment - Luxury Balls and Friend Balls provide the Pokémon with a more comfortable one than other Pokéballs
