These answers are overly complicated. You can change the main body font size (as well as any other CSS you might want to change) simply by embedding CSS directly into the Rmarkdown document using the html <style> tag. You do not need an entire CSS file for something so simple. If you are doing a lot of CSS then use a separate CSS file. If you are just modifying a couple of simple things I would do it like this.
---
title: "Untitled"
author: "James"
date: "9/29/2020"
output: html_document
---
<style type="text/css">
body{
font-size: 12pt;
}
</style>
```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```