The phrase 'it affects not only' is a correct and usable phrase in written English.
You can use it when you want to emphasize that a particular action or event will have more than one consequence or impact. For example, "This issue affects not only the environment, but also our health and our economy."
It affects not only how teachers teach but how they view their superiors and their own colleagues.
It affects not only those who failed to get on the medal platform, but those who did.
It affects not only people and their families, but also government programs, the medical profession and the economy as a whole.
It affects not only minimum-wage workers but also those paid slightly more, who often receive raises when the minimum rises.
It affects not only the carrier's extensive domestic routes, but also its 15 routes serving the United States, including New York and Los Angeles.
"When children don't get the right nutrition in the first 1,000 days – from the start of a woman's pregnancy until her child's second birthday – it affects not only their growth, but their brain development.
"It affected not only North Wilkesboro, but the entire area and other counties too," said Faye Cox, the North Wilkesboro mayor pro-tem.
Jane Lubchenco, the NOAA administrator, said the BP spill posed unusual challenges because it affected not only beaches, marshes and wildlife, but also the deep-sea environment and the ocean floor.
That decision brought with it such powerful consequences that it affected not only the education of medical students but also the lives of the countless patients we would one day treat.
As the virus spread, it affected not only humans, but other plants and animals as well, and the Earth's environment rapidly deteriorated, turning cities into desolate landscapes and the wilderness into wastelands.
