Background In addition to medication, health behavior management is crucial in patients with multiple risks of cardiovascular mortality. Objective This study aimed to examine the efficacy of a 3-month Smart Management Strategy for Health–based electronic program (Smart Healthing). Methods A 2-arm randomized controlled trial was conducted to assess the efficacy of Smart Healthing in 106 patients with at least one indicator of poor disease control and who had hypertension, diabetes, or hypercholesterolemia. The intervention group (n=53) took part in the electronic program, which was available in the form of a mobile app and a Web-based PC application. The program covered 4 areas: self-assessment, self-planning, self-learning, and self-monitoring by automatic feedback. The control group (n=53) received basic educational material concerning disease control. The primary outcome was the percentage of participants who achieved their clinical indicator goal after 12 weeks into the program: glycated hemoglobin (HbA1c) <7.0%, systolic blood pressure (SBP) <140 mmHg, or low-density lipoprotein cholesterol <130 mg/dL. Results The intervention group showed a significantly higher success rate (in comparison with the control group) for achieving each of 3 clinical indicators at the targeted goal levels (P<.05). Only the patients with hypertension showed a significant improvement in SBP from the baseline as compared with the control group (72.7% vs 35.7%; P<.05). There was a significant reduction in HbA1c in the intervention group compared with the control group (difference=0.54%; P≤.05). In the intervention group, 20% of patients with diabetes exhibited a ≥1% decrease in HbA1c (vs 0% among controls; P≤.05). Conclusions A short-term self-management strategy-based electronic program intervention may improve clinical outcomes among patients with cardiovascular risks. Trial Registration ClinicalTrials.gov NCT03294044; https://clinicaltrials.gov/ct2/show/NCT03294044