Mobility-as-a-Service (MaaS) is an emerging business model driven by the concept of ``Everything-as-a-Service'' and enabled through mobile internet technologies. A MaaS system consists of a typical two-sided market, where travelers and transportation service providers (TSPs) are two groups of agents interacting with each other through a MaaS platform. In this study, we propose a modeling and optimization framework for the regulation of two-sided MaaS markets. We consider a name-your-own-price (NYOP)-auction mechanism where travelers submit purchase-bids to accommodate their travel demand via MaaS platform, and TSPs submit sell-bids to supply mobility resources for the MaaS platform in exchange for payments. We cast this problem as a single-leader multi-follower game (SLMFG) where the leader is the MaaS regulator and two groups of follower problems represent the travelers and the TSPs. The MaaS regulator aims to maximize its profits by optimizing operations. In response to the MaaS regulator's decisions, travelers (resp. TSPs) adjust their participation level in the MaaS platform to minimize their travel costs (resp. maximize their profits). We analyze cross-group network effects in the MaaS market, and formulate SLMFGs without and with network effects leading to mixed-integer linear bilevel programming and mixed-integer quadratic bilevel programming problems, respectively. We propose customized branch-and-bound algorithms based on strong duality reformulations to solve these SLMFGs. Extensive numerical experiments conducted on large scale simulation instances generated from realistic mobility data highlight that the performance of the proposed algorithms is significantly superior to a benchmarking approach, and provide meaningful managerial insights for the regulation of two-sided MaaS markets in practice.