The mathematical function used to model cross-correlation curves in FCCS is slightly more complex compared to that used in FCS. One of the primary differences is the effective superimposed observation volume, denoted as   in which the G and R channels form a single observation volume:
where  and are radial parameters and  and are the axial parameters for the G and R channels respectively.
The diffusion time,  for a doubly (G and R) fluorescent species is therefore described as follows:
where  is the diffusion coefficient of the doubly fluorescent particle.
The cross-correlation curve generated from diffusing doubly labelled fluorescent particles can be modelled in separate channels as follows:
In the ideal case, the cross-correlation function is proportional to the concentration of the doubly labeled fluorescent complex:
with 
The cross-correlation amplitude is directly proportional to the concentration of double-labeled (red and green) species.