Il suffit de redéfinir la commande `\thesection` localement
**Edit** Ok si j'ai bien compris c'est `\thesubsection` qu'il faut redéfinir.
\includepdf[pages = 1, pagecommand = {\pagestyle{scrheadings}},
frame = true, scale = 0.9]{annexe.pdf}
{\renewcommand{\thesection}{\Roman{section}} {\renewcommand{\thesubsection}{\Roman{subsection}}
\includepdf[pages = 2, pagecommand = {\pagestyle{scrheadings}},
addtotoc={2, subsection, 2, Premi\`ere section de l'annexe, label1},
frame = true, scale = 0.9]{annexe.pdf}
\includepdf[pages = 3, pagecommand = {\pagestyle{scrheadings}},
addtotoc={3, subsection, 2, Seconde section de l'annexe, label2},
frame = true, scale = 0.9]{annexe.pdf}}
**ECM**
\documentclass[12pt, a4paper, french, BCOR = 0pt, DIV = 22]{scrartcl}
\usepackage[utf8x]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[light, largesmallcaps]{kpfonts}
\usepackage{scrlayer-scrpage}
\usepackage{lastpage}
\usepackage{pdfpages}
\usepackage{lipsum}
\usepackage{babel}
\begin{document}
\ifoot{\textsf{Titre}}
\cfoot{}
\ofoot{\textsf{\thepage/\pageref{LastPage}}}
\pagestyle{scrheadings}
\section{Introduction}
\lipsum[1]
\newpage
\section{Annexes}
\includepdf[pages = 1, pagecommand = {\pagestyle{scrheadings}},
frame = true, scale = 0.9]{annexe.pdf}
{\renewcommand{\thesection}{\Roman{section}} {\renewcommand{\thesubsection}{\Roman{subsection}}
\includepdf[pages = 2, pagecommand = {\pagestyle{scrheadings}},
addtotoc={2, subsection, 2, Premi\`ere section de l'annexe, label1},
frame = true, scale = 0.9]{annexe.pdf}
\includepdf[pages = 3, pagecommand = {\pagestyle{scrheadings}},
addtotoc={3, subsection, 2, Seconde section de l'annexe, label2},
frame = true, scale = 0.9]{annexe.pdf}}
\newpage
\tableofcontents
\end{document}
