I have RNA-seq data sets (3 control replicates and 3 treatment replicates). I have obtained intron counts for every intron in all the 6 samples(3,3). My question is can I use deseq2 on this intron count matrix just like we use it on gene counts?

Thanks

I don't see any reason why not. The typical thing to look for are whether you trust the estimation of size factors, which assumes that a large number of introns are not differentially transcribed across condition. This can be assessed in an MA plot among other plots.