Tariff barriers to cross-Strait trade are expected to be reduced under the ECFA but non-tariff measures (NTMs) will increase. NTMs are tightly connected to national administrative activities, whose nature is relatively flexible, goal-oriented, censored and discriminatory. Their effect on limiting market access is often greater than that of tariff measures. NTMs may reduce imports as the presence of NTMs may lead to higher domestic prices. The specification and application of NTMs by Mainland China should be examined to ensure fair market access for Taiwan. NTMs is an important issue in FTAs. This study attempts to quantify the effects of NTMs, with the Tobit model applied to EU and Japan due to the lack of NTMs data for Mainland China. Results indicate the potential for economic benefits from further liberalization of NTMs is likely to be substantial, therefore a future cross-Strait ECFA should be negotiated with this in mind.