Distribution discrepancy is an intrinsic challenge in existing fingerprint-based indoor positioning system(s) (FIPS) due to real-time environmental variations; thus, the positioning model needs to be reconstructed frequently based on newly collected training data. However, it is expensive or impossible to collect adequate training samples to reconstruct the fingerprint database. Fortunately, transfer learning has proven to be an effective solution to mitigate the distribution discrepancy, enabling us to update the positioning model using newly collected training data in real time. However, in practical applications, traditional transfer learning algorithms no longer act well to feature space heterogeneity caused by different types or holding postures of fingerprint collection devices (such as smartphones). Moreover, current heterogeneous transfer methods typically require enough accurately labeled samples in the target domain, which is practically expensive and even unavailable. Aiming to solve these problems, a heterogeneous transfer learning framework based on co-occurrence data (HTL-CD) is proposed for FIPS, which can realize higher positioning accuracy and robustness against environmental changes without reconstructing the fingerprint database repeatedly. Specifically, the source domain samples are mapped into the feature space in the target domain, then the marginal and conditional distributions of the source and target samples are aligned in order to minimize the distribution divergence caused by collection device heterogeneity and environmental changes. Moreover, the utilized co-occurrence fingerprint data enables us to calculate correlation coefficients between heterogeneous samples without accurately labeled target samples. Furthermore, by resorting to the adopted correlation restriction mechanism, more valuable knowledge will be transferred to the target domain if the source samples are related to the target ones, which remarkably relieves the “negative transfer" issue. Real-world experimental performance implies that, even without accurately labeled samples in the target domain, the proposed HTL-CD can obtain at least 17.15% smaller average localization errors (ALEs) than existing transfer learning-based positioning methods, which further validates the effectiveness and superiority of our algorithm.