This is what I get from this simple example:
\documentclass[11pt,a5paper,footinclude=true,headinclude=true]{scrbook}
\usepackage[T1]{fontenc}
\usepackage[linedheaders,parts,pdfspacing]{classicthesis}
\begin{document}
This is inline math $a+b=c$ and a displayed formula follows:
\[
\int_{-\infty}^{\infty}e^{-x^2}\,dx=\sqrt{\pi}
\]
\end{document}
The font used for math is MathPaZo, which is tailored to accompany the default Palatino text font.
If I change the example in the following way
\documentclass[11pt,a5paper,footinclude=true,headinclude=true]{scrbook}
\usepackage[T1]{fontenc}
\usepackage[linedheaders,parts,pdfspacing,eulermath]{classicthesis}
\begin{document}
This is inline math $a+b=c$ and a displayed formula follows:
\[
\int_{-\infty}^{\infty}e^{-x^2}\,dx=\sqrt{\pi}
\]
\end{document}
(note the eulermath option), I get Euler Math for the formulas.
If instead you load lmodern after classicthesis
\documentclass[11pt,a5paper,footinclude=true,headinclude=true]{scrbook}
\usepackage[T1]{fontenc}
\usepackage[linedheaders,parts,pdfspacing]{classicthesis}
\usepackage{lmodern}
\begin{document}
This is inline math $a+b=c$ and a displayed formula follows:
\[
\int_{-\infty}^{\infty}e^{-x^2}\,dx=\sqrt{\pi}
\]
\end{document}
you get the "standard" LaTeX fonts
Best Answer
Why don't use the option
eulermathforclassicthesis? The Euler font for math is really nice.MWE
Output
Anyway, if you really want Computer Modern as the math font, add the following lines in your preamble
MWE:
Output