Unbounded Petri nets (UPNs) can describe and analyze discrete event systems with infinite states (DESIS). Due to the infinite state space and the combination explosion problem, the reachability analysis of UPNs is an NP-Hard problem. The existing reachability analysis methods cannot achieve an accurate result at reasonable costs (computational time and space) due to the finite reachability tree with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\omega$</tex-math> </inline-formula> -numbers. Based on the idea of approximating infinite space with finite states, given some limited reachable markings of a UPN, we propose a method that can quantitatively solve the UPN’s reachability problem with machine learning. Firstly, we define the probabilistic reachability of markings and transform the UPN’s reachability problem into the prediction problem of markings. The proposed method based on positive and unlabeled learning (PUL) and bagging trains a classifier to predict the probabilistic reachability of unknown markings. Finally, to predict the markings outside the positive sample set and unlabeled sample set, an iterative strategy is designed to update the classifier. Based on seven general UPNs, the results of the experiments show that the proposed method has a good performance in the accuracy and time consumption for the UPN’s reachability problem. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —In discrete event systems, the reachability problem mainly studies reachable states of the system and the relationship between states, which is the basis of the system’s states, behaviors, attributes and performance analysis. For discrete event systems with infinite states, it is hard to analyze the reachable relationship between states within a finite time due to the infinite state space and the combination explosion problem. The main motivation of the paper is to propose a method that can predict the reachable relationship between the states with a probability value within a finite time. By machine learning algorithms, the method learns the feature information of the known reachable states. The reachability of unknown states in the infinite state space can be predicted approximately. The proposed approximation method can be applied to analyze the reachability properties of general discrete event systems with infinite states, such as checking whether a fault occurs in operating systems, whether a message is delivered in communication and so on.