Insomnia disorder with objective short sleep duration (less than 6 h of objective sleep or sleep efficiency less than 85%) has been considered as a biologically severe subtype of insomnia associated with a higher risk of cardiometabolic disease morbidity. This systematic review and meta-analysis firstly compared insomnia disorder with objective short and normal sleep duration, and subsequently, objective short sleep duration with and without insomnia disorder, and their associations with hypertension, type 2 diabetes and body mass index. A systematic search of five databases yielded 2345 non-duplicated articles, of which 11 individual studies were used for the qualitative review and 10 individual studies for the meta-analysis. The sample size varied from 30 to 4994 participants. A higher risk of hypertension (RR 1.54, 95% CI: [1.30; 1.82] p < 0.0001) and type 2 diabetes (RR 1.63 [1.37; 1.94], p < 0.0001) was associated with insomnia disorder with objective short sleep compared to normal sleep duration, but not for body mass index. Comparisons between insomnia disorder with objective short sleep and objective short sleep without insomnia disorder showed no significant differences. However, the majority of these studies were cross-sectional, and there is a need for more cohort study data.