Introduction: The majority of Filipino households experience food insecurity. Mothers and children are among the population groups suffering from poor diet quality. This study aimed to determine the extent of the association of household food security (HFS) to mothers’ and children’s dietary diversity score (DDS), and to identify the significant factors associated with meeting the DDS of these vulnerable groups. Methods: The study was a cross-sectional, population-based study utilising secondary data from the 2015 Updating Survey. From a total of 6,692 mother-child pairs, the association between HFS and meeting the DDS of mothers and children, as well as the potential predictors for meeting the DDS were tested using descriptive and logistic regression analyses. Results: The findings showed that HFS was significantly associated with meeting the DDS of mothers and children aged 6-36 months (p<0.001). The proportion of meeting the DDS among mothers and children was significantly higher in food-secure than in food-insecure households (20.7% vs. 14.4%). Furthermore, meeting the DDS decreased with increasing levels of food insecurity. Household food security status, education background, employment, child’s age, and wealth status were significantly associated with meeting the DDS. Conclusion: This study showed the extent of how food security was associated with meeting the DDS of mothers, children, and mother-child pairs, and the factors associated with meeting the DDS. Results can be used to strengthen the formulation of appropriate, evidence-based policies to address household food insecurity and low DDS among mothers and young children.