Most proteins are intrinsically fluorescent to some extent due to the presence of tryptophan residues. There are also flavoproteins, which may be fluorescent due to the presence of a flavin prosthetic group. There are also phycobiliproteins, which contain fluorescent pigments.

Article Phycobiliproteins: Structural aspects, functional characteri...

Thanks @ Adam. I only know phiLOV2.1 which has a different strucrue and smaller size than GFP.

Dear Yufei Hu

You can try to use the DsRed or eqFP578 group fluorescence proteins which have different structures than GFP. DsRed group includes mRFP, mCherry, mPlum, etc, whereas eqFP578 group includes TagRFP, TagBFP, mKate, etc. You can check this link: https://www.fpbase.org/lineage/

Best wishes.