Skin on my pubic bone and penis is brown. i started using clotrimazole 1% on my penis and pubic bone and around 40% of that brown color & spots cleared but i've been using it for 3 months. should i continue using it ? is it bad using it for so long ?

You shouldn't need to use Clotrimazole for more than 6 weeks. If you have light and dark areas that clear with an antifungal, you may be dealing with tinea versicolor. If that's the case, it usually clears in the winter because of less sun exposure, but in the summer the infected areas stay lighter while other areas tan. You won't know until next summer if it worked.

If it is helping then continue. There is no harm as the local application is not absorbed