Recently, diffusion-based recommendation methods have achieved impressive results. However, existing approaches predominantly treat each user's historical interactions as independent training samples, overlooking the potential of higher-order collaborative signals between users and items. Such signals, which encapsulate richer and more nuanced relationships, can be naturally captured using graph-based data structures. To address this limitation, we extend diffusion-based recommendation methods to the graph domain by directly modeling user-item bipartite graphs with diffusion models. This enables better modeling of the higher-order connectivity inherent in complex interaction dynamics. However, this extension introduces two primary challenges: (1) Noise Heterogeneity, where interactions are influenced by various forms of continuous and discrete noise, and (2) Relation Explosion, referring to the high computational costs of processing large-scale graphs. To tackle these challenges, we propose a Graph-based Diffusion Model for Collaborative Filtering (GDMCF). To address noise heterogeneity, we introduce a multi-level noise corruption mechanism that integrates both continuous and discrete noise, effectively simulating real-world interaction complexities. To mitigate relation explosion, we design a user-active guided diffusion process that selectively focuses on the most meaningful edges and active users, reducing inference costs while preserving the graph's topological integrity. Extensive experiments on three benchmark datasets demonstrate that GDMCF consistently outperforms state-of-the-art methods, highlighting its effectiveness in capturing higher-order collaborative signals and improving recommendation performance.