Cortical interneurons can be categorized into distinct subtypes based on multiple modalities; however, it remains unclear to what extent these modalities are correlated. In this study, we collected morphological, electrophysiological and molecular expression data in L5 interneurons of the mouse somatosensory cortex (S1) using Patch-PCR, aiming to reveal the correlations between molecular marker expressions and morpho-electric properties. An integrated classification procedure based on extracted morphological and electrophysiological features yielded 11 major morpho-electric subtypes (M/E types). Molecular cell groups were defined by either the differential expressions of neurochemical markers (neurochemical cell groups, NC groups) or the high expression of specific transcriptomic signatures (transcriptomic cell groups, TC groups). We found that, although at the subclass level (Pvalb, Sst, Vip and Non-Vip), most interneurons had distinct morpho-electric properties, distinctions were relatively weak between individual NC groups and TC groups. Moreover, similar results are also obtained in L5 interneurons of V1 and M1 using recently published Patch-seq data and a comparable analysis approach. Interestingly, compared to S1 and M1, the degree of correlation between TC groups and morpho-electric properties is significantly higher in V1. Finally, direct comparison of TC groups across different brain areas suggested that L5 interneurons of S1 were morpho-electrically more similar to M1 compared to V1. Overall, this comprehensive multimodal correlation analysis in S1 and systematic comparison between S1, V1 and M1 provide new insights about the morpho-electric correlates of molecularly defined cortical interneuron populations.