Multiple GNSS antennae systems have been among the well-known approaches to attitude determination of moving platforms in recent years. However, the constraints on the onboard GNSS antennae configuration, that is, installing the antennae baselines along the main axes of the platform, can lead to practical difficulties and inevitable uncertainty. In this article we present an iterative method to obtain the accurate attitudes by means of the onboard misaligned baselines. In order to remove the effects of the horizontal and vertical misalignments from differential GNSS observations, attitude-induced corrections have been developed through the relative lever-arm coordinates of the onboard antennae. This approach provides us with more freedom from spatial distribution of the onboard antennae. The performance of the proposed method has been analyzed by simulated data and an actual experiment in low- and high-dynamic situations. The simulation has been designed to evaluate the capability and reliability of the iterative method under the presence of small and large misalignments. The field experiment was carried out in the offshore waters of Kish harbor using three dual-frequency GNSS receivers with choke-ring antennae onboard a survey vessel, which was also equipped with an inertial measurement unit (IMU). The maximum allowable misalignments, the convergence of the iteration, and the advantage of the proposed method over the trigonometric approach in spite of applying the traditional calibration are presented. The long-term stability of GNSS attitude determination as well as IMU accuracy degradation, due largely to the increase in the time-varying biases/noises, have demonstrated the potential of the method to estimate the accuracies and biases of the onboard inertial sensor. The overall results have affirmed that the proposed method can effectively provide the platform attitudes using the misaligned GNSS baselines with as much flexibility as possible for the onboard antennae configuration.