\documentclass[border=1mm]{standalone}

\usepackage{cmap}
\usepackage[cp1250]{inputenc}	
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{lmodern}
\usepackage{tikz}
\usepackage{float}
\usepackage{siunitx}
\usepackage{amsmath}
\usepackage{upgreek}
\usepackage{pgfplots}
\pgfplotsset{compat=1.17}
\usepgfplotslibrary{units}
% \makeatletter
%\pgfplotsset{
%  unit code/.code 2 args=
%    \begingroup
%    \protected@edef\x{\endgroup\si{#2}}\x
%} 
%\makeatother

\pgfkeys{%
  /tikz/on layer/.code={
    \pgfonlayer{#1}\begingroup
    \aftergroup\endpgfonlayer
    \aftergroup\endgroup
  }
}

\begin{document}
	\begin{tikzpicture}
	
		\begin{axis}[
			name=main plot,
			height=5cm,	width=10cm,	grid=major,
    		y unit=\SI{}{\volt},
			ylabel={$V_\mathrm{CPO}$},
			xmin=0, xmax=400,
			ymin=0.55,ymax=0.61,
			%xtick distance = 250e-12,
			ytick distance = 0.01,
			%ytick = {0.55,0.56,0.58,0.6,0.61},
			set layers,
			%x tick label style={/pgf/number format/.cd, set thousands separator={}},
			xticklabel shift = 2 pt,
			legend pos=north east,
			xticklabels =\empty,
			scaled x ticks = false,
			xlabel =
		]		
			
			\addplot +[solid, smooth,thick,color=blue,mark=none] table [x expr=\thisrow{cvox}*1e9,y expr = \thisrow{cvoy}, col sep=semicolon] {../cadence_data/dll_wvfs.csv};
			\label{cvo};
			
		\end{axis}
		
		\begin{axis}[
			%scale only axis,
			height=5cm,	width=10cm,			
			ymin=-10,ymax=50,
			xmin=0, 
			xmax=400,
			ytick distance = 10,
			%ytick = {-10,0,20,40,50},
			axis y line*=right,
			axis x line=none,			
			y unit=\SI{}{\pico\second},
			ylabel={FPD $t_\mathrm{in}$},
			%legend pos=north west
			legend style={at={(0.7,0.5)},anchor=west}
			]
			
			\addlegendimage{/pgfplots/refstyle=cvo};
			\addlegendentry{$V_\mathrm{CPO}$};
			\addplot +[solid, smooth,thick,color=red,mark=none] table [x expr=\thisrow{phasex}*1e9,y expr = \thisrow{phasey}*1e12, col sep=semicolon] {../cadence_data/dll_wvfs.csv};			
			\addlegendentry{FPD $t_\mathrm{in}$};
			
		\end{axis}
		
		\begin{axis}[
      		at={(main plot.below south west)},
      		height=5cm,	width=10cm,	grid=major,
      		anchor=north west,    % <-- added
      		yshift=1ex,          % <-- adjusted
      		xmin=0, 
      		xmax=400,
      		ymin=570,ymax=630,
      		ytick distance = 10,
      		%xtick distance = 250e-12,
      		ylabel=ILRO $f_\mathrm{0}$,
      		y unit=\SI{}{\mega\hertz},
      		xlabel = $t$,
      		x unit = \SI{}{\nano\second},
      		%xticklabels =\empty,
			scaled x ticks = false,
			legend style={at={(0.5,0.4)},anchor=north}
      		]
      		
      		\addplot +[solid, smooth, thick,color=blue,mark=none] table [x expr=\thisrow{ilox}*1e9,y expr = \thisrow{iloy}*1e-6, col sep=semicolon] {../cadence_data/dll_wvfs.csv};     		
      		
    	\end{axis}
		
	\end{tikzpicture}
\end{document}