We provide a definition of Vafa-Witten invariants for projective surface Deligne-Mumford stacks, generalizing the construction of Tanaka-Thomas on the Vafa-Witten invariants for projective surfaces inspired by the S-duality conjecture. We give calculations for a root stack over a general type quintic surface, and quintic surfaces with ADE singularities. The relationship between the Vafa-Witten invariants of quintic surfaces with ADE singularities and the Vafa-Witten invariants of their crepant resolutions is also discussed. CONTENTS 2.1. Surface DM stacks, examples 2.2. Moduli space of semistable sheaves on surface DM stacks 2.3. The moduli space of Higgs pairs 3. Deformation theory and the Vafa-Witten invariants 3.1. Deformation theory 3.2. Families and the moduli space 3.3. The U(rk) Vafa-Witten invaraints 3.4. SU(rk) Vafa-Witten invariants 3.5. C ˚-fixed loci 4. Calculations 4.1. Root stack on quintic surfaces 4.2. Quintic surfaces with ADE singularities 4.3. Discuss on the crepant resolutions Appendix A. The perfect obstruction theory, following Tanaka-Thomas A.1. The perfect obstruction theory for U(rk)-invariants A.2. Deformation of Higgs fields 1 2