We introduce HarmonySet, a comprehensive dataset designed to advance video-music understanding. HarmonySet consists of 48,328 diverse video-music pairs, annotated with detailed information on rhythmic synchronization, emotional alignment, thematic coherence, and cultural relevance. We propose a multi-step human-machine collaborative framework for efficient annotation, combining human insights with machine-generated descriptions to identify key transitions and assess alignment across multiple dimensions. Additionally, we introduce a novel evaluation framework with tasks and metrics to assess the multi-dimensional alignment of video and music, including rhythm, emotion, theme, and cultural context. Our extensive experiments demonstrate that HarmonySet, along with the proposed evaluation framework, significantly improves the ability of multimodal models to capture and analyze the intricate relationships between video and music.