Stock market is an essential element of financial market, therefore, the study on volatility of stock market plays a significant role in taking effective control of financial market risks and improving returns on investment. For this reason, it has attracted widespread attention from both academic circle and related industries. However, there are multiple influencing factors for stock market. Facing the multi-source and heterogeneous information in stock market, it is challenging to find how to mine and fuse multi-source and heterogeneous data of stock market efficiently. To fully explain the influence of different information and information interaction on the price changes in stock market, a graph neural network based on multi-attention mechanism was proposed to predict price fluctuation in stock market. First of all, the relationship dimension was introduced to construct heterogeneous subgraphs for the transaction data and news text of stock market, and multi-attention mechanism was adopted for fusion of the graph data. Then, the graph neural network Gated Recurrent Unit (GRU) was applied to perform graph classification. On this basis, prediction was made for the volatility of three important indexes: Shanghai Composite Index, Shanghai and Shenzhen 300 Index, Shenzhen Component Index. Experimental results show that from the perspective of heterogeneous information characteristics, compared with the transaction data of stock market, the news information of stock market has the lagged influence on stock volatility; from the perspective of heterogeneous information fusion, compared with algorithms such as Support Vector Machine (SVM), Random Forest (RF) and Multiple Kernel k-Means (MKKM) clustering, the proposed method has the prediction accuracy improved by 17.88 percentage points, 30.00 percentage points and 38.00 percentage points respectively; at the same time, the quantitative investment simulation was performed according to the model trading strategy.