3D reconstruction in dynamic scenes primarily relies on the combination of geometry estimation and matching modules where the latter task is pivotal for distinguishing dynamic regions which can help to mitigate the interference introduced by moving objects. Furthermore, the matching module explicitly models object motion, enabling the tracking of specific targets and advancing motion understanding in complex scenarios. Recently, the proposed representation of pointmap in DUSt3R suggests a potential solution to unify both geometry estimation and matching in 3D space, but it still struggles with ambiguous matching in dynamic regions, which may hamper further improvement. In this work, we present POMATO, a unified framework for dynamic 3D reconstruction by marrying pointmap matching with temporal motion. Specifically, our method first learns an explicit matching relationship by mapping corresponding RGB pixels across different views to 3D pointmaps within a shared coordinate system. Furthermore, we introduce a temporal motion module for dynamic motions that ensures scale consistency across different frames and enhances performance in tasks requiring both precise geometry and reliable matching, most notably 3D point tracking. We show the effectiveness of the proposed pointmap matching and temporal fusion paradigm by demonstrating the remarkable performance across multiple downstream tasks, including video depth estimation, 3D point tracking, and pose estimation.