Guided weapon systems operating in maritime environments, such as the Vertical Launch System (VLS), form a core element of modern naval capabilities. Although vertical launch provides an advantage in confined spaces, the dynamic motion of the platform (ship) is directly transferred to the launch vehicle until just before launch, making navigation initialization challenging. Weapon systems deployed on offshore platforms are continuously affected by environmental disturbances such as waves, wind, and currents, as well as the ship's propulsion and steering. Consequently, assuming a stationary initial state when estimating the weapon's attitude using an Inertial Measurement Unit (IMU) introduces significant limitations. The process of determining this initial attitude, known as alignment, is critical in IMU-based navigation systems. Errors in initial attitude estimation directly propagate through the entire guidance phase. This leads to accumulated navigation errors and ultimately degrades missile accuracy. Although Global Navigation Satellite System (GNSS) updates can correct navigation solutions during the midcourse phase, IMU-based inertial navigation is indispensable during the early post-launch phase-before GNSS data become available. Moreover, GNSS corrections may be unavailable in jamming or spoofing environments. It is therefore important to accurately determine the initial attitude and rapid transition to inertial navigation mode to ensure the required guidance performance of ship-launched missiles. This study compares and analyzes three representative alignment methods applicable to maritime environments: one-shot alignment, one-shot mixed alignment, and shipboard transfer alignment, under identical sea conditions. To quantitatively reflect the dynamic nature of the marine environment, simulation data based on wave conditions were generated using the Marine System Simulator (MSS). The initial alignment accuracy of each method was evaluated using these data, and the subsequent inertial navigation performance was analyzed. From the obtained results, one-shot mixed alignment, which utilizes missile-mounted IMU acceleration data, exhibited large alignment errors due to hull motion effects, while transfer alignment using attitude and velocity data from the Master Inertial Navigation System (MINS) achieved higher accuracy. It was confirmed that in high sea state conditions, the transfer alignment method utilizing continuous velocity and attitude information from the MINS provided the highest performance in estimating the missile's attitude.