Mobility as a Service (MaaS) is an innovative solution for improving transport systems and has gained significant attention in recent years. With the development of MaaS, the additional utility provided by offering packaged services is considered a key factor in attracting users, meaning that evaluating the added value of MaaS bundles becomes a critical issue for MaaS providers. Motivated by this, we proposed a novel approach for evaluating the added value of MaaS bundles considering heterogeneous subscription willingness. First, we develop an Integrated Choice and Latent Variable (ICLV) model to capture the factors influencing user subscription to MaaS bundles and to estimate the subscription willingness of different users. Building upon the estimations, we identify the user groups with different subscription willingness to MaaS bundles and further evaluate the added value of MaaS bundles considering their heterogeneous subscription willingness. The proposed approach is tested using collected data from a stated preference survey conducted in Beijing, China. The results estimated by the ICLV model offer some insights from Beijing. Furthermore, the identification of target users of these four designed MaaS bundles shows that the target users of public-transportation-oriented (PT-oriented) bundles have higher subscription willingness. As for the estimated added values, the estimated added value of the metro-oriented bundle is highest, followed by that of the bus-oriented bundle. Furthermore, the stability analysis of the added value is also conducted and verifies the robustness of the proposed approach. These findings help formulate the pricing scheme of the entire MaaS bundle and suggest that formulating MaaS bundles based on the PT-oriented philosophy may help increase the penetration rate of MaaS and the profitability of MaaS providers.