  Understanding the origins of small-scale flats of CCDs and their
wavelength-dependent variations plays an important role in high-precision
photometric, astrometric, and shape measurements of astronomical objects. Based
on the unique flat data of 47 narrow-band filters provided by JPAS-{\it
Pathfinder}, we analyze the variations of small-scale flats as a function of
wavelength. We find moderate variations (from about $1.0\%$ at 390 nm to
$0.3\%$ at 890 nm) of small-scale flats among different filters, increasing
towards shorter wavelengths. Small-scale flats of two filters close in central
wavelengths are strongly correlated. We then use a simple physical model to
reproduce the observed variations to a precision of about $\pm 0.14\%$, by
considering the variations of charge collection efficiencies, effective areas
and thicknesses between CCD pixels. We find that the wavelength-dependent
variations of small-scale flats of the JPAS-{\it Pathfinder} camera originate
from inhomogeneities of the quantum efficiency (particularly charge collection
efficiency) as well as the effective area and thickness of CCD pixels. The
former dominates the variations in short wavelengths while the latter two
dominate at longer wavelengths. The effects on proper flat-fielding as well as
on photometric/flux calibrations for photometric/slit-less spectroscopic
surveys are discussed, particularly in blue filters/wavelengths. We also find
that different model parameters are sensitive to flats of different
wavelengths, depending on the relations between the electron absorption depth,
the photon absorption length and the CCD thickness. In order to model the
wavelength-dependent variations of small-scale flats, a small number (around
ten) of small-scale flats with well-selected wavelengths are sufficient to
reconstruct small-scale flats in other wavelengths.
