He didn't deliberately poison himself. Alchemy involves a lot of nasty experimentation with lead, antimony, mercury, and other substances that, depending on what you do with them (e.g., burning them, melting them, combining them with acids and bases that release gases, etc.), can pose real human health hazards. Alchemical work was in particular associated with lead, which is bad enough, but many of the other things they used were not great things to be exposed to in a world without serious precautions (no fume hoods, no real knowledge of what they were doing). Huffing mercury and lead fumes is not good for the brain.
Newton's own alchemical work was in search of the Philosophick Mercury, sometimes called the Philosopher's Stone, thought to be the substance that would allow for the power to transmute elements into one another, and thus to become a kind of Chemical God (which would grant, among other helpful things, the famous ability to transmute base metals into gold, but also immortality, since decomposition and death are also chemical processes).
With Newton, it should be noted that there is a lot of overlap in his alchemical interests and his "regular" scientific interests, like optics. He did not see these things are being entirely separate topics. Nor did he see any of them as being separate from his theological interests, which were at least as extensive as his scientific pursuits.
A lot of the alchemical experiment we have records of today involve alchemists recreating unusual arrangements of chemicals, with names like the "Philosopher's Tree" and "Philosopher's Egg" and "The Net" and "The Star Regulus" and so on. Chemists and historians today have recreated some of these and figured out what exactly what was going on. Lawrence Principe's The Secrets of Alchemy (U. Chicago Press, 2013) is in particular quite interesting in this regard, showing the kinds of work that went into being an alchemist, and the kinds of obscure chemical structures they labored to create. (From the book, here is an image of a "Philosopher's Tree" made of mercury and gold).
Deciphering Newton's own interests is difficult because the writings he made on the work he did in alchemy are always incomplete, were not done with standardized equipment or with high-precision tools, and are largely written in alchemical code (e.g., "Dissolve the volatile Green Lion in the central salt of copper and the Green Lion is distilled from this spirit. The Blood of the Green Lion, Venus, the Babylonian Dragon interposing his poison in all things overcome by the beating of Diana's Doves, the Bond of Mercury" — this sounds like nonsense but it is actually an explication of a chemical procedure, and figuring out what it means in modern terms takes a LOT of historical and chemical knowledge. "Volatile Green Lion" might be some kind of acid compound, for example.). So understanding his work, his goals, and how they played into his interests in physics and theology is the work of many scholars who study him.
