This article analyzes the extent to which ambiguity and uncertainty affect Taiwanese public opinion toward future cross-Strait relations. With respect to different conditions for future integration across the two sides of the Taiwan Strait, we adopt a set of survey questionnaires to explore Taiwanese unification-independence preferences. Then, by assuming that the latent sampling distributions of such preferences may comprise different means and unequal variances, we form a set of heterogeneous choice models to investigate the factors that may contribute to explaining the differences among means (i.e., differences among locations of responses) and the factors that may result in variations in the variances (i.e., differences among distributions of responses). Our findings are mainly three-fold: first, a respondent’s Taiwanese identity and assessment of mainland China’s economic prospects as well as political development have significant impacts in terms of determining his/her unificationindependence preference. Second, a respondent could form ambivalent attitudes toward future cross-Strait relations due to his/her conflicting (or competing) values regarding cross-Strait relations. Finally, the more knowledge (or information) about cross-Strait issues a respondent possesses, the less uncertain he/she may become when expressing his/her unification-independence preference. However, this uncertainty argument is not fully supported by our empirical data.