The class Yathesis will equalize the height of the logos. You can change the height of particular logo with logoheight as in \institute[logoheight=1cm, logo=images/ulco]{ULCO}
In this example the logos are in the sub-directory images. They have very different heights, as it can be seen, but they appear top and bottom aligned in the title page.

ComUE.jpg (140x119)

Institut.jpg (688x190)

CoInstitut.jpg (942x264)

Download the three images in a sub directory images of your working directory, change their names and try this code.
\documentclass{yathesis}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{kpfonts}
\begin{document}
\author[aa@zygo.fr]{Alphonse}{Allais}\title[Laugh’s Chaos]{Le chaos du rire}
\subtitle[Chaos’ Laugh]{Le rire du chaos}
\academicfield[Mathematics]{Mathématiques}
\speciality[Dynamical systems]{Systèmes dynamiques}
\date{15}{8}{2021}
\submissiondate{1}{10}{2020}
\subject[Chaotic Laugh]{Rire chaotique}
\doctoralschool[url=http://edspi.univ-lille1.fr/]{ED Régionale SPI 72}
\comue[logo=images/ComUE,url=]{ComUE Lille Nord de France} % <<<<<<<<<<<<<<
\institute[logo=images/Institut,url=]{ULCO}% <<<<<<<<<<<<<<
\coinstitute[logo=images/CoInstitut]{Université de Paris~13}% <<<<<<<<<<<<<<
\laboratory[
logo=,
telephone=,
fax=,
email=,
url=
]{{LMPA Joseph Liouville}}{%
\
\
\
\
\
}
\maketitle
\end{document}