The general best practice is to use the thickest possible air filter for maximum efficiency. But, never try to force an air filter into a space it's not designed for. If you attempt to use a 4-inch thick air filter for a system that is made for a 1-inch thick filter, the efficiency will be worse. The short answer? A 4-inch filter will last longer and provide better air quality for your home.
First, 4-inch filters cover a higher range of MERV ratings, with some overlap with 1-inch filters. With a filter of 4, you'll get at least an 8 MERV rating. With higher ratings of up to 16, you can control supermicro contaminants such as bacteria, viruses and dust particles. Most HVAC professionals will tell you that thicker filters perform better than common 1-inch oven filters.
Thicker filters, known as media filters, are usually 4 to 5 inches thick compared to ubiquitous 1 inch filters that you can even buy at grocery stores. All filters have a MERV rating, which marks the efficiency of the filter in removing contaminants from the air supply. And while media filters produce more airflow (less pressure drop) and clog less easily, you should be careful with the MERV rating. On the other hand, 1-inch filters are decent enough to remove typical dust, pet dander, and other particles up to 3 microns in size.
That's a technical way of saying “how many and how small particles it filters out of the air you breathe. The MERV rating is basically a measure of how well the filter captures particles in the 0.3 to 10 micron size range. If your HVAC systems currently work with a filter 1, a filter 4 will not be able to fit in the existing cabinet. The more and smaller particles a filter traps, the faster it will fill with dust, pollen, pet hair and dander, etc. Particularly vulnerable parts include the air controller or oven blower motor that works overtime to push and draw air through the dirty filter and the heat pump or compressor air conditioners responsible for circulating the refrigerant between the outdoor and indoor units.
Poorly fitted one-inch filters where air passes around the frame (even causing the frame to bend and deform) are very common. These media filters have much stiffer cardboard frames, and some media filters even have plastic “rails” on the top and bottom so you can slide them inside the oven with a very tight seal. 1-inch pleated air filters have higher MERV ratings for one simple reason: they have more surface area to trap particles. Regardless of length and width, it is the thickness that determines the surface area of the filter.