Hi, I'm new in biological analysis.

I want to use DESeq2 to do my analysis, I have batch 1 and batch 2, and the batch equals group.

If I want to remove the batch effect, should I only use design = ~ group + condition, or I should use design = ~ batch + group + condition ?

And this is PCA result, is there any batch effect exist? Should I remove batch effect before WGCNA?

You can use either group or batch (if you ensure it's a factor first), but not both. For WGCNA you should convert from counts using one of the methods in this section of the vignette.. You may also want to remove the batch effect after that (or maybe you can use blind = TRUE if the design is just ~ group. But WGCNA isn't a Bioconductor package, so this isn't really the place to get help for that package.