No. Per the worksheet in publication 936, you aggregate your mortgage balances and your interest for the calculation, so effectively, it will be a blended interest rate. You can't choose to solely deduct one or the other.
https://www.irs.gov/pub/irs-pdf/p936.pdf
**Note, there is a provision that allows you to treat a mortgage as "not secured by your home" for tax purposes. That would (in theory) allow you to declare that the loan on your main home is not secured by the home and therefore not eligible for the interest deduction, therefore the interest deduction would only be based on the mortgage on the second home. This treatment is usually only used when the home is used for business and you plan to deduct the mortgage interest as a business expense, or if you want to take out a second mortgage/HELOC and use it to buy some kind of investment, and you want to use the investment interest deduction instead of the mortgage interest deduction. The decision to treat a mortgage as "not secured by the home" can't be reversed unless you get permission from the IRS, so if you make this election, you can never again treat your main home mortgage as deductible, even if you sell the second home. So I would not do this without extremely competent professional advice.
