  The measurement of pulsar pulse times-of-arrival (ToAs) is a crucial step in
detecting low-frequency gravitational waves. To determine ToAs, we can use
template-matching to compare each observed pulse profile with a standard
template. However, using different combinations of templates and
template-matching methods (TMMs) without careful consideration may lead to
inconsistent results. In pulsar timing array (PTA) experiments, distinct ToAs
from the same observations can be obtained, due to the use of diverse templates
and TMMs. In other words, employing diverse approaches can yield different
timing results and would thus have a significant impact on subsequent
gravitational wave searches. In this paper, we examine several commonly used
combinations to analyze their effect on pulse ToAs. we evaluate the potential
impact of template and TMM selection on thirteen typical millisecond pulsars
within the European PTA. We employ pulsar timing methods, specifically the root
mean square and reduced chi-square $\chi_r^2$ of the residuals of the best
timing solution to assess the outcomes. Additionally, we evaluate the
system-limited noise floor (SLNF) for each pulsar at various telescopes
operating around 1.4~GHz using frequency-resolved templates.
  Our findings suggest that utilizing data-derived and smoothed templates in
conjunction with the Fourier-domain with Markov-chain Monte Carlo (FDM) TMM is
generally the most effective approach, though there may be exceptions that
require further attention. Furthermore, we determine that pulse phase jitter
noise does not significantly limit the current precision of the European PTA's
timing, as jitter levels derived from other studies are much smaller than the
SLNF.
