The registration between indocyanine green angiography (ICGA) and multi-color scanning laser (MCSL) imaging fundus images is vital for the joint linear lesion segmentation in ICGA and MCSL and the evaluation whether MCSL can replace ICGA as a non-invasive diagnosis for linear lesion. To our best knowledge, there are no studies focusing on the image registration between these two modalities. In this paper, we propose a framework based on convolutional neural networks for the multimodal affine registration between ICGA and MCSL images, which contains two parts: coarse registration stage and fine registration stage. In the coarse registration stage, the optic disc is segmented and its centroid is used as a matching point to perform coarse registration. The fine registration stage regresses affine parameters directly using jointly supervised and weakly-supervised loss function. Experimental results show the effectiveness of the proposed method, which lays a sound foundation for further evaluation of non-invasive diagnosis of linear lesion based on MCSL.